


The Colonel's Daughter

by crzy_wrtr10



Category: Stargate Atlantis
Genre: Alternate Universe, Angst, Emotional Hurt/Comfort, Episode Related, Episode Remix, Family, Family Secrets, Father-Daughter Relationship, Feels, Fluff, Gen, Kid Fic, M/M, Minor Character Death, Miscommunication, Parenting for Beginners, Sheppard has a kid, Some Humor, Stealth Crossover, Team Dynamics, Team as Family, Tooth-Rotting Fluff
Language: English
Status: In-Progress
Published: 2014-03-03
Updated: 2014-03-03
Packaged: 2018-01-14 10:51:45
Rating: Teen And Up Audiences
Warnings: Creator Chose Not To Use Archive Warnings, No Archive Warnings Apply
Chapters: 8
Words: 55,093
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/1263571
Author URL: https://archiveofourown.org/users/crzy_wrtr10/pseuds/crzy_wrtr10
Summary: <blockquote class="userstuff">
              <p>Through a series of mishaps, John and the daughter he didn't know he had are reunited.</p>
<p>And it changes everything.</p>
            </blockquote>





	1. Arrival: Welcome to Atlantis

**Author's Note:**

> This was (is, still is, it's still going) my first major multi-chapter fic. I started it my first year of college (first posted on ff.net in May 2009) and it's still going. 
> 
> This might be the kick in the ass I need to get moving with it again. 
> 
> Anything you recognize I probably don't own. Ali is my OC, I've probably taken liberal liberties with a lot of things, and the chapters that are episode based/episode rewrites will be labeled. There is, eventually, some brief mentions of slash between Evan Lorne and David Parrish (because I just can't help myself, I swear) and there are lots of fluffy and family-oriented feelings all around. Eventually. It takes them a little while. 
> 
> Not beta'd. Any mistakes you find feel free to point and cackle.

“I’m not your personal lamp-lighter, Rodney,” John protested, hands on his hips. He’d been ensconced in the lab for what seemed like hours, handling device after device to see what worked. It was getting old. 

“Today, Major, you’re a lightsocket on legs,” McKay shot back, handing John yet another hand-held device. “Just accept your fate and move on.”

“It’s Colonel, Rodney,” he sighed, exasperated. He knew that Rodney knew about his promotion, he’d most certainly congratulated him, but it was a funny little sticking point between the two of them. John found he got a chuckle out of it and knew Rodney got a smile. But still… “A ‘lightsocket on legs’?” John arched an eyebrow in typical Sheppard fashion.

Rodney turned a bit pink. “It’s just an expression.”

John rolled his eyes with a snort. “Sure.”

McKay was about to respond when John was paged through his earpiece. “Sheppard here.”

_"The_ Daedalus _is here, sir. Colonel Caldwell needs to speak with you in Dr. Weir’s office. Immediately."_

“I’ll be right there.” John looked at Rodney who merely shrugged. So far as he knew, John hadn’t gotten himself into anything – no trouble on Atlantis, no trouble off-world. He’d been the poster-boy for model behavior. To say both he and Rodney were clueless as to why Caldwell would need to speak with him was an understatement. And so urgently, too.

“I’ll see you at dinner?” Rodney asked. It had slowly become their tradition over the time that they’d been in Atlantis.

“Yeah,” John said, backing out the door. “See you later.” He walked quickly from Rodney’s lab toward the main tower. It was a quick trip, thanks to a transporter, and the first he noticed in the Gateroom was the feeling of unease. Everyone seemed subdued, as though all hell was about to break loose. Sure that would happen quite a bit whenever the _Daedalus_ was docked, but this was a little ridiculous. Entering Elizabeth’s office wasn’t much better. In fact, it was almost disturbing – Elizabeth sat behind her desk, hands folded, a file folder in front of her. Caldwell stood against the wall, sharing Elizabeth’s calm but veiled expression. Truthfully, it was like someone had died.

“Sit down, John,” she said softly. 

The use of his first name threw him a little, but he sat in one of the two chairs in front of her desk. It was almost a throwback to his younger days when he was used to sitting before the principal trying to explain his latest “stunt”, but in this situation it was anything but fun. He sat straight in the chair, hands in his lap.

“There’s really no easy way to say this, John,” Elizabeth said, her eyes full of sadness, “but three weeks ago the SGC received word that Nancy, you’re ex-wife, passed away abruptly while on the job. I’m sorry.”

John felt as though he’d been sucker-punched in the gut and he slumped in his seat. Dead. His ex-wife was dead. He’d loved her passionately at one point, and though he still loved her in a way, it had been better for them to go their separate ways. To realize now that she was ultimately gone hurt worse than he would have ever predicted. He looked at her, seeing her sympathy for his pain. Looking over at Caldwell piqued his curiousity. Why, exactly, the Colonel was there was still a mystery. He didn’t need to have come if all they had to speak to him about was his ex-wife’s death.

“There’s more,” she said, drawing John away from his thoughts. “Nancy had a very explicit will.” She glanced briefly at Caldwell. “Among instructions of what to do with her material possessions, there are also specific instructions about Alison.” She looked at John.

“Who’s Alison?” John asked. Last he knew, he didn’t think his ex-wife had any sort of pet. Maybe it was a dog? He had to admit that it was a fairly funny picture in his head of a dog running through Atlantis, maybe taking a bite out of a few Wraith.

Caldwell snorted derisively.

“What?” John was genuinely confused.

Elizabeth took a deep breath, opened the file folder on her desk, and handed out to John an evelope. John took the envelope with a sense of foreboding and opened it. Inside was a 4x6 photograph of a teenage girl and a dog sitting beneath a tree. She had long, dark, wavy hair, but it was the eyes that spoke to John. She had hazel eyes. Hazel with a hint of green. He looked up at Elizabeth, on the brink of realization and then it dawned. He shook his head, almost trying to deny what was ultimately happening.

“Yes, John,” she said, “that’s Alison. Alison Sheppard. Your daughter.”

John threw the picture onto the desk and lowered his head to his hands. He had a kid? A teenager, now, apparently. His teenager. His girl. Why had Nancy never told him? Didn’t she think he would make a good father? No, probably not since she’d said at one point that he was married to the Air Force first and that she was his affair. And how the hell had she hit the fact that she was pregnant? Was he _that_ oblivious? Apparently he had been. But if he had a daughter there was no way he’d be able to stay on Atlantis. He’d have to go back to Earth and take care of her. That’s when his second epiphany hit him. Caldwell was there to take his place, that’s why the Colonel had come. 

Already knowing the answer, John rasied his head and asked, “What else does the will say?”

Elizabeth glanced at Caldwell and then looked at John. “She was very specific stating that Alison was to be left in your care since you’re the father. There is nothing that we can do about that, and it’s probably the best thing to do in the long run.”

There it was then. His life on Atlantis was over. He’d have to go back to Earth.

“ _But_ ,” she emphasized, “there is another specific set of instructions stating that you are not to be removed from Atlantis. Personally, I would truly like to know how she got the authorization that she did, but that’s another matter. 

John could barely believe what was happening. He was staying on Atlantis, but had to take care of Alison? How was that going to work? Unless… “She’s coming here?” John squeaked. This was beginning to get overwhelming.

“The SGC ruled that to comply with all parts of the will, Alison would come to Atlantis,” Caldwell said. “On one condition.”

Sheppard wasn’t sure he wanted to know but asked anyway. “Which was?”

“She doesn’t go back to Earth unless you do.”

John felt as though the air had been sucked from the room. He remembered vividly the feeling of isolation those first few awkward months had provided, just the expedition members and an abandoned city. The idea that Alison could never go back to Earth, never see anything familiar again, was monumental. There was no way to predict how she would react to a one-way trip she had no opinion on. She had the potential to hate a father she didn’t even know before she’d ever met him just because she’d been forced to give up everything she’d ever known. In that position, John would hate himself, too.

“So,” John said with a tight smile. “When does she arrive?”

Elizabeth and Caldwell shared another glance. John felt unease creep into the room. 

“She’ s on the _Daedalus_ ,” Caldwell said. “We can beam her down when you’re ready.”

_Yeah, well, what if I’m never ready?_ John thought, swallowing hard. Might as well get the first contact over with. “I’d like to meet her alone. This first time.” He did first contact missions for a living with alien cultures on distant planets. This was his own child. How much more difficult and awkward could it be that he hadn’t already faced before?

“Understandable,” Elizabeth said, closing the folder and standing. She gave him a small, encouraging smile on her way by. “My office is your office. Take as much time as you need.” Closing the door behind her left John and Caldwell in the room together. The other Colonel tapped his earpiece and then was engulfed in a beam of white light. He was gone in seconds, giving John another chance to mull things over in his head. Was she going to hate him on contact or would she let it fester until it consumed them both? She was a girl. Girls incubated feelings worse than boys. He stood and watched a beam of white light appear again. When it was gone, it left a teenage girl in the middle of Elizabeth’s office. There was a dark blue rolling suitcase next to her, a backpack on her back, a cardboard box in her arms, and her eyes were closed. Her hair was in a ponytail; she was dressed in blue jeans and a sweatshirt. She was fairly short, only about 5’4. 

“Am I there yet?” she asked timidly. 

John smiled. Only a Sheppard would do something like that. “Yup. You’re here.”

Slowly, Alison opened her eyes. She took a look around the room and finally let her gaze settle on John. She took him in; hazel eyes, flamboyant hair, the silver chain of his dogtags and a look on his face that said he was just as freaked out about meeting her as she was meeting him. Slowly, she put the box down and walked over to him, leaving a few feet of space between them. This was her father, the man she’d seen in photographs. He looked more caring in person than he did in the photos back home on the fireplace. 

She grimaced. That wasn’t home anymore. Atlantis (boy was that weird to think about) was where she lived now. Lived. But couldn’t you live someplace that wasn’t home?

The silence stretched between the two of them, uncomfortable and loud.

“I’m Lieutenant Colonel Jonathan Sheppard,” John said, trying to ease the tension. “I’m your –“

“I know who you are, Colonel –“ she began.

“John.” He looked at the floor while she bit her lip. He couldn’t ask her to call him “dad,” not when it was so foreign a concept to the pair of them. That had to be something that evolved when they learned and trusted each other. That was a stage further on down the road, if they ever got that far. He wasn’t going to push it. He swallowed, his throat suddenly dry. “Call me John.”

She smiled thinly. “I’m Alison.” She paused and gave him a tiny portion of a real smile. “Call me Ali.” She held out a hand. John shook it.

“So,” she said, not so much to keep the conversation going to so as to avoid the awkward silence, “this is Atlantis, the lost but found city of the Ancients?” There was skepticism in her voice, but also a hint of laughter.

John knew he’d heard those words before, somewhere. He looked at her oddly. “Were you hanging out with Daniel Jackson before you came here?”

“Just a few hours,” she said. “He’s an interesting person.” She looked at the floor again. “Is this really the city of the Ancients?” There was a challenge in her eyes when she looked at him next.

“Yes, it is,” he said calmly. “Would you like a tour?”

Ali looked through the glass doors to her right and knew that everyone out there was wondering what was going on, wondering who she was. She felt like a spectacle.

“You’ll see some really cool stuff.”

Silence. Then, “Okay.”

John smiled, hoping that Atlantis would take to Ali the same way that the city had taken to him. Opening the door to the office for her, he let her step through. She left her backpack by the door.

“This is the Gateroom,” John explained, motioning to all the consoles and work stations. He pointed to a man at a console with strangely-lettered keys on it. “That’s Chuck. He dials the ‘Gate when we go out and checks our identification codes when we come home.” Yes, it was a deliberate use of the word home in hopes to personalize things for her, but it was true. He led her to the balcony that overlooked the Stargate. She froze when she saw it. It was the most unique thing that she’d ever seen before. 

And then it began to spin.

“Off-world activation,” Chuck called to John. “It’s Major Lorne returning early.”

Ali watched in fascinated silence as the chevrons locked and the wormhole punched its way into existence. It had just replaced her previous thought of the coolest thing she’d ever seen. She jumped a little when four figures came through the puddle. 

“That’s Major Lorne and his team,” John said. “So it’s Lorne, Cadman, Ruiz, and Parrish. Lorne is also my Executive Officer.”

Ali nodded and followed when John tugged gently on her arm. She got a few stares on the way out and felt her cheeks redden. She hadn’t feeling like an outsider. John showed her the cafeteria, a few of the labs (she even briefly met the force of nature that was Rodney McKay on coffee), the gym, the transporter (he demonstrated to her the basics and then had her use it) and finally they stopped outside a door. 

“I live here.” That was all John said and opened the door. It was a small room but it was uniquely his. That much Ali could tell immediately. A guitar in the corner, a Johnny Cash poster, he liked music. But he read, too. There was a copy of _War and Peace_ on the desk next to his laptop. She briefly wondered what kind of email service she would be able to get. This room probably spoke more about John than anything else in Atlantis, but she didn’t know. She didn’t know anything about him in the sense that he also knew absolutely nothing about her. 

She looked at him and realized he was waiting for some sort of reaction. “It’s nice.” She looked around again, realizing that she was more than a little homeless. For the first time in her life she had no idea where she was going to sleep that night.

“John?”

“Ali?”

“Where am I sleeping?” She didn’t mean to sound so lost and alone, but that’s how it sounded. 

“We’ll find you a room,” he said. He was still trying to wrap his mind around the fact that he had a daughter, that she was on Atlantis and could never go back to Earth. She seemed so lonely that he wanted nothing more to hold her. He was going to make a move to do so when he thought that she wouldn’t want it. Maybe not that she wouldn’t want it, but she wouldn’t accept it yet. “Eventually.”

Ali looked at him in confusion. 

“You’ll have your own room eventually, but maybe it’s better for these first few nights if you stay here with me. There’s a fold-up cot floating around somewhere.”

She smiled, unsure if she loved that idea of having him close her first nights, or if she wanted her space. What she really wanted to do, deep down, was to go home to her mother and the way things used to be. 

“It’ll take a few nights to get used to the different noises,” he said, “but you’ll get used to it.”

Ali wished she could believe him, but found it hard to. It was hard to take confidence in someone who wasn’t so sure about the idea that he was coming up with. She might not have known him, but she could read him pretty good already. And it was only the beginning.

 

_It’s freshman year all over again,_ Ali thought as she threaded her way through the cafeteria, feeling every stare in the flush of her cheeks and the conversations that started as she passed. She was the stranger in the room, an outsider in the midst of a family unit. She had a moment of panic when she realized she’d lost track of where John had gone and then she calmed herself. All she needed to look for was the flamboyant fly-boy hair. After a moment of straining her neck to see, she found him at a table in the back. With three other people. 

Oh. Damn.

She’d had courage when she’d gotten the news that her mother had been killed, she’d had courage to sit in front of Colonel O’Neill and learn that she was heading on a two week voyage into deep space on a space ship, of all things, and she had courage to sit on said space ship for two weeks with people she didn’t know, she could sure as heck find the courage to sit with John and his friends. Taking a deep breath, she approached the table with confidence and a small, if timid smile.

John pulled out the chair next to him for her, leaving her no choice but to sit. She could do this. She put her tray down with shaky hands and sank into the chair. She recognized the man on John’s left as Rodney McKay, the scientist she’d met earlier. The other two, a woman with soft features and a mountain of a man with the best, wildest mane she’d ever seen, eyed her curiously. She tried for a smile and got a wobbly attempt.

Sheppard cleared his throat. “This is Ronon,” he motioned to the moutain main across from her, “Teyla,” the woman next to him, who nodded her head, “and you met Rodney already.” 

“Yes, yes, we’ve met,” Rodney said, his attention never leaving his food. “Very fascinating.”

“Hello,” Ali squeaked. She was nervous. And from the tenseness of John’s shoulders, he wasn’t exactly all calm and cool, either. 

“This is Ali,” John continued. He took a deep breath. Ali flushed a little; John did the same. “She’s my daughter.”

Rodney took a gulp of whatever he was drinking and tried to breathe at the same time resulting in water all over the table and great hacking coughs. It was rather comical, actually, because John knew that he wasn’t really choking. Teyla arched an eybrow and Ronon’s expression didn’t change. McKay’s hacking became a sort of background noise. 

“I – I did not know you had a daughter, John,” Teyla said. Ali flushed even darker and stared at her plate. So she hadn’t known much about John, about her father, but she’d at least thought that he’d known about her. She got Christmas cards and Birthday cards from him every year, didn’t she? Her mom would always look for the smile that was on her face when she opened them. But no one in John’s life knew about her. She was beginning to get the impression that _he_ didn’t even know about her before she had physically arrived. Which hurt worse than anything she’d ever felt, including leaving her entire old life behind. 

“I – uh, I – “

Listening to John stammer through an explanation was bad. Her cheeks flaming, tears in her eyes, she looked at her hands in her lap. Her mother had left her, her father didn’t want her or know about her, what was left? 

“You had a kid and you didn’t know about her?”

John groaned inwardly and glared at Rodney. Trust McKay to say the wrong thing at the wrong time in the wrong situation. Looking over at Ali, he was shocked to see her barely holding it together. He opened his mouth to try to explain, but the look on his face was all that she needed. Feeling isolated, unwanted, and alone, she pushed her chair back violently, stood and ran from the table, tears in her eyes. 

“Ali? Alison! Wait!” John went to stand up without pushing his chair back first and rammed his knees into the underside of the table. It was too late, anyway, she was gone. “Damn it!” He turned to Rodney who had the grace to look shamefaced. “Damn it, Rodney, why couldn’t you have kept your mouth shut?”

“You’re blaming _me_?” Rodney yelped. “ _You’re_ the one who didn’t know he had a daughter until she was in Atlantis! And why is she here, Colonel? Who did you sleep with that you pissed off completely and they sent her here?” His voice was rising.

“She’s _my_ daughter with my ex-wife and she’s here because Nancy’s dead!” John wasn’t aware that their conversation had gotten very loud until he’d said the last part and was met with silence. Closing his eyes, he tried to regain his composure and stem the headache that was threatening to engulf him. He put his head in his hands, elbows on the table, and tried to get a handle on everything that was going on. “I didn’t know. I do, now, though. She lost her mom three weeks ago. Nancy’s last will was explicit that she come and stay with me, but also explicit that I stay in Atlantis. As the result, she can’t ever go back to Earth because of what she knows, what she’s seen.” He sighed and looked at his untouched food. “I’ve known her less than a day and I’ve already screwed this up.”

Rodney, wisely, kept his mouth shut. 

“It takes time, John,” Teyla said. “She’s hurting because of the loss of her mother, and she’s feeling abandoned because she’s in a completely new world to her. Give her some time and space but let her know that you are there. She will need you, John. Just give her some time.”

“I don’t even know where she is, Teyla,” he said. 

She smiled in her all-knowing Athosian way. “The city loves you, John. She’ll help you find your daughter.”

 

When Ali stopped running she realized she had no idea where to go or even where she was. It was then that she knew she was a mess. It wasn’t just the tear-tracks down her cheeks or her messy hair, it was that she was completely disoriented and alone. She was still hurting inside from the loss of her mother, the hurt of being left alone in the world with no one to care for her. Moving had been rough. It wasn’t like moving to a new city, or a new house or apartment. In reality, she’d moved to a new _galaxy_. It was a completely new culture. A completely new way of life that she’d have to get used to and she knew absolutely no one. 

And then there was John. Her father. He was her father in the sense that she shared his DNA but other than that they held nothing in common. She realized with a sad dawning that he’d never sent her any cards or letters. It had been her mother faking it, to make her think that John knew about her and loved her and that the only thing that separated them was distance. Ali had believed that he’d loved her, when in reality he hadn’t even known she existed. 

Wiping her cheeks with the sleeve of her sweatshirt, she started walking again. She couldn’t hide forever. Sooner or later she’d have to face John again. It was inevitable. Not only was he her father, but he was also her guardian. He was the one who was going to take care of her and part of her accepted that. But it was just so hard to trust him because he didn’t even seem to care. It was a lot to process, on both ends, and she knew that things were changing dramatically for him as well. 

She wandered on through the hallway, trying to empty her mind and just think about nothing for a few minutes. Pausing, she leaned against the wall and yelped when it slid aside and she fell through onto the floor. Great. She hadn’t even been on her own for an hour and she’d already busted something. Pushing herself to her feet she dusted herself off and looked around. It was a little too dark to see anything properly. If only there were lights…She jumped when the room turned the lights and consoles on by itself. Great. The city was no only extremely old and partially abandoned, but had ghosts, too.

“It’s because you have the gene.”

Ali couldn’t help it; she jumped and screamed, whirling around with a hand on her chest to keep her heart in. John stood in the doorway, leaning against the jamb like it was his job. 

“I’m sorry I scared you,” he said, taking a step into the room. She searched his eyes; he was sincere.

“It’s okay,” she said when she caught her breath. “How did you find me?”

He pulled a squarish device from his pocket and showed her the screen. It held two white dots. “It’s a life-signs detector. You can find people with it.” He handed it to her and the screen went dark. 

“It turned off,” she said, looking at him. “How do you turn it on?”

“Think on.”

She looked at the device in her hand and thought “on.” To her absolute amazement the screen lit back up. There was a real grin on her face when she looked up at John. “I made it work!”

He smiled at her happiness. “Yes, you did. Your gene did. See, there’s a certain gene that certain people posess that allows them to operate Ancient technology. But, thanks to Carson, Dr. Beckett, that is, who created a gene therapy, more people have the gene to a varying degree. My gene is natural, whereas Rodney’s isn’t.”

Ali’s eyes lit up with the absorption of the new knowledge. “So, my gene is natural?”

“Yes,” John said. “Because you were born with it.” He tucked his hands into his pockets and looked into a set of eyes the same color as his own. “I’m sorry.” He swallowed. “I’m sorry that I didn’t have the privelege of knowing you before I met you.” He watched her lower lip wobble. “I’m sorry that you spent two weeks on a starship with a bunch of people you didn’t know and that this has been a rough month. Which, now that I think about it, is probably an understatement.” The tears had come back to her eyes but he needed to continue. He needed to get this off his chest so they could start fresh and start to build something from the ground up. “I’m sorry for the loss of your mother. I know she meant so much to you.” Ali took a step toward him. This next part was crucial because, according to what John knew, no one had told her that there was no going back. “And I’m very, very sorry that you can’t ever return to Earth.”

“What?” Ali was dumbstruck. A small, illogical part of her brain had held onto the fact that she was from Earth originally and that she could, after spending some time with John to satisfy what she understood to be conditions in her mother’s will, she could eventually go back and stay with somebody else. She didn’t want to force John into anything more painful than what they’d already been forced into. But to hear from him that there was no going back, that it was a one-way trip, positively broke her heart.

John caught her when her legs gave out and pulled her close, rocking her gently back and forth as she sobbed. She sobbed out all her pain, frustration, fear, and antyhing else that she’d been feeling and suppressing since being told of her mother’s death. When she was absolutely exhausted, she fell asleep against his chest, completely worn out. He simply picked her up and headed for the transporter. He ignored the stares and wondering glances of those he passed in the hallway finally made it to his room. Once there, he put her on his bed and gently tucked her in. She was his daughter, a concept new to the pair of them, but it was a fact. It wasn’t going to go away. 

_And I thought Rodney was the only thing that could change so much in so little time,_ he thought. Rodney was a force of nature that he took off-world, but Ali was her own force that had stormed into his life, just like he had stormed into hers and changed everything. _But you, girl, are something else._ He pushed a strand of her hair back and gently kissed her forehead. He straightened, and then went to the door to the balcony, opening it slightly. The gentle lapping sound of waves was a soft background noise and the light breeze brought a fresh scent with a hint of salt. These were the smells and sounds of Atlantis, the smells and sounds of Alison Sheppard’s new home. 

 

The first thing that Ali heard when she woke up in the morning was the gentle sound of waves. After two weeks of hearing the hum of an engine, waves was a nice contrast. She looked around at all that was different; the room layout, the desk, and even though Johnny Cash staring down at her was a little creepy, it all reminded her of John. The place even smelled like him, which, when she thought about it, was perfectly reasonable. He’d been there a long time before her. Atlantis was his home. 

_Yours too, if you let it,_ the voice in her head whispered. Throwing back the covers, she stood and stretched. There on the desk, between the computer and _War and Peace_ was a walkie-talkie and a note. 

_Ali,_

_Your suitcase and other things are in the room, over by the the closet. The walkie-talkie is so that you can find me or talk to me whenever you need to. It’s set to an open channel, so you may catch some other conversations as well. I’ll meet you for lunch at 1 in the cafeteria but until then, feel free to wander a little bit. Get your bearings. However, STAY OUT of the unexplored/uncleared parts of the city. I’ll see you at lunch._

_-John_

She ran her hand over the walkie-talkie and debated about saying good morning. Instead, she went about her typical morning routine (minus the shower since she didn’t even want to attempt to operate it because it looked a little complicated and she didn’t want to flood anything) and then, walkie-talkie in hand, headed out the door into the hallway. The hallways were surprisingly light and airy and she smiled. That was until she was nearly run down by a stampeding group of Marines. At least they didn’t stare which was a plus for them in her book.

It was after she’d wandered the same hallway three times that she realized not only was she hungry, but she was also lost. She stared at the walkie-talkie. And pressed the button. “John?”

_”John who?”_

She couldn’t tell if that was John Sheppard or somebody else. “John Sheppard?”

_”You need to say who you are and who you’re paging, Ali.”_ That was definitely John Sheppard.

“So, Ali Sheppard to John Sheppard?” She smiled despite of herself. This was kind of fun.

_”Much better. Sheppard here._

“I’m lost. And I’m hungry.” It might have sounded pitiful but she didn’t care. Her stomach got the best of her when she was hungry.

_Where are you?_

Ali looked around for anything that might give her a clue as to where she was. “No idea.”

There was a rush of static from the walkie-talkie that was definitely a snort. _Alright. Sit tight, I’ll have somebody come get you. Sheppard out._

She stared at the device in her hand again and giggled. She’d just had a conversation through a walkie-talkie with John. She was still smiling when a man in the same type of uniform that John wore stepped around the corner and stopped in front of her.

“Alison Sheppard?” he asked. 

Ali nodded mutely; the man broke into a smile.

“I’m Evan Lorne, John’s Second in Command,” he said, extending his hand for her to shake. “We’re embarking on a mission to find the cafeteria?” He looked serious but there was a smile in his eyes. Ali liked him already and nodded. “Right, well, we’ll start by going this way.”

She walked beside him and it was almost like taking a tour he was so informative and helpful. Ali knew twice as much as she did previously by the time they got to the cafeteria. And she also knew about him. He loved to paint in his spare time (which was rare) and generally seemed to be a very likeable person. He even went through the lunch choices with her and told her (voice low and very discreet under the watchful eyes of the kitchen staff) what foods to stay away from and which to grab before everybody else. She settled on some cereal and a glass of orange juice and didn’t have a problem finding a table since most of them were empty. 

“Thank you for the help, Major Lorne,” she said politely with a small smile. His company had been enjoyable. 

“Evan,” he said with a nod. “And you’re welcome. Enjoy your breakfast.”

Ali sat at the table by herself, ate her breakfast in silence, and watched the people come in and out of the cafeteria. She could tell who was a soldier and who was a scientist pretty easiliy; soldiers were usually on a mission (no pun intended) when it came to getting food, and the scientists were usually distracted. They either brought their work with them, or grabbed something easily ate on the go and were out the door as soon as they walked through it. About twenty minutes after she’d finished her meal and was bored with people watching, she really wished for a good book. Heck, even John’s beat up copy of _War and Peace_ would have been fantastic. Instead, she propped her elbows on the table, set her chin on her hands, and went back to watching the people.

“Alison?”

She didn’t jump as high as she had the previous time someone had snuck up on her. Turning, she saw it was the woman that John had been sitting with the previous night. Teyla, her name was. Ali smiled. “Hi Teyla.”

“May I sit with you?”

“Sure.” 

Teyla sat gracefully in the chair across from Ali. For a moment the two merely studied each other. There was a moment of silence and then Teyla said, “I am sorry for our dinner conversation last night. We were assuming that John knew he had a daughter and were hurt that he would not have told us. I am sorry if you were hurt because John did not know, either.” There was such sincerity in Teyla’s eyes that even if she wanted to be mad at the woman, she couldn’t. Teyla hadn’t done anything wrong; it wasn’t her fault that Ali and John hadn’t met before. It was beyond Teyla’s control. 

“It’s not your fault,” Ali said, wishing she had something to occupy her hands and divert her attention from the uncomfortable conversation. “I thought that John knew about me.” She looked away as tears came to her eyes. She had the feeling that no matter how many times she talked about this, it would still be hard to stomach. “It’s not your fault that he didn’t.” She smiled and looked at Teyla’s kind eyes. “But I’m sure that if he had known, he would have told you.” 

Teyla smiled. “How was your first night here in Atlantis?”

Finally, something mundane and normal to talk about. Well, as normal as someone from a completely different galaxy asking about the first night of the your permanent stay in a once-abandoned city. “It’s got some different noises than what I’m used to, but I’ll adjust. The waves are really soothing at night.” It was the truth – she’d gone to bed with the background noise of the waves and had woken up to the sounds of gently lapping water. Very soothing for the troubled mind. “I’m more used to traffic sounds, so it’s really quiet here.” Maybe that was a little further than she’d like to go, but it was okay. Ali had the feeling that Teyla was more like family to John than just a teammate. And then there was the feeling of trust. Ali had the concrete feeling that she could _trust_ Teyla was just about anything. 

“It was difficult for me as well to move to Atlantis.” She smiled gently at Ali’s confused frown. “I used to live on the Mainland with the rest of my people. We are called Athosians.” Her voice and expression turned a little more serious. “Things changed when John and the others arrived. He accidentally woke up the Wraith. And until it was safe to return to the Mainland, many Athosians stayed here in Atlantis.” She didn’t want to explain too much because she didn’t know how much John wanted her to hear, how much he wanted her to know. So she’d given Ali an abridged version of what had happened, and figured that if she wanted more details, she would go to John. It would be a good bonding experience for the pair of them. 

“Wow,” Ali said. The Athosians had been a little homeless, in a way. “So you were kind of like me, in a way. You didn’t really know what to expect?”

“Exactly. But we adjusted quickly.” 

If a number of Athosians could stand relocation for a little while, Ali could most certainly make the best of her new situation. Or so she reasoned.

 

John met her for lunch at one, just like he’d said in his note to her, and together they munched on turkey sandwiches and pudding cups. He told her about his morning (pretty much that he’d been doing paperwork he couldn’t foist onto Lorne) and trying to organize his hole-in-the-wall office so that it resembled some sort of order when he took her by to give her a little look-see later. Which he somehow connected to swinging by the infirmary. 

“What? Why?” she asked, taken aback. She knew there was an infirmary in Atlantis, there had to be, but she didn’t think she’d have to be seeing it unless she got sick. 

“Doctor Beckett wants to give you a physical, draw some blood, ask you some questions,” John said nonchalantly with a shrug. “Just the usual to get a little bit of background on you. You have your own file now.”

She smiled thinly. Great. That’s exactly what she wanted to do. She wanted to get stuck with needles by some doctor to figure out that she was fine. The rational part of her mind understood, logically, what it was for. The other part of her brain was outraged and terrified. She hated needles with a passion. She had a few burning questions she wanted answered, one of them being, “Are you coming with me?”

John looked up from his sandwich and swallowed. “Yeah. I can come in with you.” He narrowed his eyes. “Are you afraid of doctors?”

She narrowed her eyes right back at him. “No.” She paused. “I just don’t like needles, that’s all.” 

John got that “uh huh” look on his face and nodded. “Doc Beckett’s real good at quick sticks with a needle. You’re in good hands.” He smiled.

She smiled back and then stared at her non-appealing pudding cup. _Fabulous. Absolutely fabulous._

 

Her very first impression of Dr. Carson Beckett wasn’t a visual one. It was what she heard. 

“How many times have I told yeh that yeh need to be careful with particularly acidic alien plants?” came the semi-angry, semi-exasperated Scottish brogue from behind a curtain to Ali’s left. She was sitting on a bed, legs dangling and swinging back and forth like an impatient/worried/bored teenager. John was sitting next to her in a chair, completely healthy (which was apparently a rare thing) and quite calm. 

“Keep that clean and come see me tomorrow.” 

Ali had a moment of extreme nervousness when the curtain was pulled back and then pulled shut again as quickly. The only difference was that Doctor Beckett was now on her side, a smile on his pleasant Scottish features. She gave him a small smile in return. 

“Alison?” he asked. She nodded. “It’s wonderful to meet yeh. I’m Carson Beckett, the Chief Medical Officer here in Atlantis.”Another handshake. Ali was becoming quite competent at shaking people’s hands. “Well, lass, I’m going to do a simple physical, take some blood, and then yeh’ll be outta here unless yeh need to come back fer anything. Sound good?”

_The quicker, the better._ Ali thought and nodded. The first part of the physical passed just fine (she passed with flying colors) but it was the second part that was giving her the willies. When Carson snapped on a pair of gloves and asked her to pull her sleeve up out of the way, Ali was incredibly nervous and scared. The hand that wasn’t attached to the arm nearest to Carson was fisting the sheet on the bed in hope to remain calm. She closed her eyes. She couldn’t look as he prepared the needle. She jerked when he swabbed the area with disinfectant.

“Are yeh all right?” he asked her in a soft voice. 

She opened her eyes and nodded. Seemingly satisfied, he went back to swabbing down the crook of her arm. Once more reaching for the sheet, she encountered something different. Something warm and living. She wrapped her fingers around John’s and squeezed. He squeezed back, not as hard, but enough to let her know that he was there and that she wasn’t alone. There was a pinch in her arm but she focused instead on the feel of John’s hand. There were calluses on his palms, probably from his firearm, and his fingers were long and slender. He had pianist hands. 

“There yeh go,” Carson said, applying a piece of gauze and some tape to her arm. “Yeh’re all set.”

Ali looked over at Carson and smiled, her fingers still compusively wrapped around John’s. Looking at John, she immediately let go and felt as though she was drifting. In that little moment she’d felt anchored and secure. Now that security was gone she felt a little on the lonely side. When she finally looked over at John, he was still lounging in the plastic chair and looking at her. He raised his eyebrows. 

“I don’t like needles,” she said, hopping down off the bed. “Never have, never will.”

John thought about it for a moment. “I don’t like bugs. And there’s a really interesting story that I’ll tell you if you’re nice to me.” His tone might have been serious, but there was a smirk in his eyes. Ali felt hers widened in response. “I’m up for story night.” 

“Well,” John said. “It’s a little bit of a long story…”


	2. Arrival: Integration

**Summary for the Chapter:**

> John and Ali struggle to find common ground between them, though she finds a kindred spirit of sorts in a fairly unlikely place when Sheppard goes off-world for the first time since her arrival.

**Notes for the Chapter:**

> There is going to be a lot of this uploaded at one time - I don't write _that_ fast, but I do have about 17 chapters worth of this already. And formatting here is rather painless. It's great.

As it turned out, the really long but really interesting story about the Iratus bug was just that: really long and really interesting, and it gave Ali some insight into the type of man that John was. After all, who in their right mind would allow themselves to be hit with a defibrillator to kill themselves to kill the bug attached to their neck, and then have enough unmoving faith in the medical team that they would revive him, to get hit again. It was confusing to her, but helpful. 

Slowly, over the course of the next week, Ali adjusted to a schedule. Breakfast was on her own, usually with Teyla, sometimes with Teyla and Ronon, and sometimes with a scientist with fly-away hair named Zelenka. He was a hoot and a half in the morning, usually because he’d been up nearly all night and dealing with McKay. Dealing with Rodney, he’d said one morning, could drive a person to either drink or have a desire to jump off the nearest high flat surface into the ocean. She thought he was serious until she saw the mischeif in his eyes. Still, she realized that Rodney McKay was his own force of nature.

After breakfast she’d wander for a little bit, stopping into random labs to see what was going on, who was doing what. It was quite memorable one morning when she popped her head into the gym and found John flat on his back, Teyla standing over him with Ronon holding up a nearby wall in his nonchalant way. Ali had been similarily impressed and amazed that a woman as small and petite-looking as Teyla could lay somebody out like that. It had been Ronon who’d spotted her. John hadn’t even attempt to ignore the fact that he’d been upended by Teyla (it apparently happened frequently) and instead had asked her if she wanted to watch. From there it was “I think I can do that” and before she knew it, Ali was taking self-defense lessons from Teyla twice a week. 

Lunch was always with John. At first their conversations were stilted and filled with uncomfortable silences, but it slowly progressed to where Ali would ask a questions about somebody or some aspect of Atlantis, John would do his best to answer. Then he started asking questions about her and her life before Atlantis. She clammed up a little and he backed off, wanting to give her space. He was aware that she was still processing all that had happened to her, especially the death of her mother. That was a subject that they had skirted widely. John knew enough not to push her particularly hard in that area. So he stayed with safe topics. Like sports.

“Do you play a sport?” he asked, taking a bite of his turkey sandwich. 

“I did,” she said, unscrewing the cap on her bottle of water. “I played soccer and ran track. What about you? You look like a cross country type of guy.” She smiled.

“I played some football,” John said. “And I like to run.” His expression turned thoughtful. “Ronon and I go running pretty much every morning. It’s a good pace, but you’re more than welcome to come with us.” 

_And be embarrassed completely by both you and the Mountain Man? Yeah, gee, thanks,_ Ali thought while plastering a smile on. “I’ll think about it.” That was a good answer. Not a yes, not a no, but something in between. It was a maybe. 

The silence stretched a little, but it wasn’t uncomfortable. John cleared his throat and then said, “I’m returning to full duty tomorrow. My team gates out at ten.”

In all honesty Ali had been wondering when something like that would be happening. She knew that he had a job to do on Atlantis, that he was on the flagship team for a reason. That was something she couldn’t prevent, something she had to learn to deal with. It had to happen sooner or later. He’d taken a week already to get her adjusted. A week was plenty, right?

“Okay,” she said, fiddling with her pudding cup. “How long are you going to be gone?” She ran what she’d just said through her mind. “I mean, when do you think you’re coming back or does it depend on where you’re going and what you’re doing?” She was babbling and probably making a fool of herself, but she didn’t really care. She just wanted to know some specifics. 

“Tomorrow’s mission should be real simple. We’re just looking to trade with some simple farmers,” he said. He smiled wryly. “I should be home in time for dinner.”

That made her feel better, but she was still worried. And the more she sat and thought about it, she was more worried for him going through the ‘Gate into the unknown than she was for her to be by herself completely for a day. 

 

She watched John, Teyla, Rodney, and Ronon step through the puddle the next morning. John looked back at her just before stepping through and waved, which made her smile. She could practically hear the “awwws” being thought among the crew but didn’t care. When the wormhole disengaged she stuck her hands in her pockets and looked around. What was she going to do with herself? If she had been back on Earth, she would have gone back to her room and started doing homework. But she didn’t really have homework anymore. She had sort of hands-on experimentation from some of the scientists in their spare time. 

Radek. He never minded when she came down for a visit. And maybe he had stuff to do that involved the Ancient gene. She could always just stand around and turn on devices for him. Not very fun on her end, but sometimes he said cool things in Czech. She was also slowly learning some Czech and the other languages spoken among the expedition members. That was one of the beest parts about living with such a diverse group of people; learning the customs and languages was a big part of understanding people. She’d figured that out a while ago, but about an hour with Daniel Jackson had cemented the idea. 

She wandered through the hallways until she got to the lab that Radek and Rodney did most of their work in. Rodney’s workspace was empty because he was off-world but Radek was gathering some of his tools and computer. 

“Going somewhere?” she asked.

The little Czech man jumped and turned to berate whoever it was that had startled him. When he saw it was Ali, his expression changed to a smile. “Little Sheppard, what are you doing down here?”

“John’s on a mission,” she said, her hands in her pockets again. “So I thought I could come see what you were up to.” Her eyes were pleading with him to let her come along, even though she didn’t say it. 

“I am going to ‘Jumper bay because one of them has malfuctioning system,” he said, slinging his bag over his shoulder. “Why don’t you come too.” His grin turned positively devious. “I teach you to hotwire ‘Jumper.”

Hotwiring anything sounded absolutely amazing in terms of fun. Her smile must have showed it. “That sounds really, really cool.” She couldn’t keep the excitement out of her voice as she followed him from the lab down to the ‘Jumper bay, one part of Atlantis that she hadn’t seen before. She’d heard John use the term Puddlejumper before, and he’d explained it, but he hadn’t showed her. Considering how most of Atlantis knew how he felt about the Puddlejumpers (and anything that flew through the air and went over 200 miles per hour), she was a little hurt that he hadn’t showed her. She pushed that to the back of her mind and felt her eyes widen at her first site. They were incredible. Something so unique and different, but like what she was used to on Earth. She was used to fighter jets that went over every Fourth of July, but there was something more about these crafts, something more genuine and creative. 

Radek opened the back hatch of a ‘Jumper and allowed her to go in first. Her head needed to be on a swivel to see all that was in there she was so curious. She went through the ‘Jumper to the cockpit and sat in the pilot’s chair. Flying something that went absurdly fast was something that was second nature to John. She looked at the consoles and display, was momentarily confused, and then decided that when John got back, had some free time, he needed to teach her how to fly. 

“So what’s it take to fly one of these?” she asked, getting out of the pilot’s seat and walking back to where Radek was. He’d pulled one of the panels off the wall and was hooking some sort of hand-held device to one of the wires. 

“The gene,” Radek said, reading the display on the device. “Because Colonel Sheppard has gene, do you have it?”

She smiled and sat on one of the benches, watching him work. “Yeah. From what Doctor Beckett says my gene is almost as powerful as John’s.”

If Radek thought it odd that she referred to her father by his first name, he didn’t let on. “If you have the gene, you can drive ‘Jumper. More difficult that turning on life-signs detector, but not overly complicated.” He poked at a wire with a screwdriver. “Has Colonel Sheppard taught you to drive yet?”

Ali really hoped he was referring to the Puddlejumper and not an actual car. She had her permit and had scheduled to take her road test when everything kind of went to hell. Ignoring that, she looked the seat cover and said, “He hasn’t. This is the first I’ve actually seen the ‘Jumpers.” It was hard to keep the hurt from her voice but she thought she succeeded. 

“Ah.” He poked another wire. “Come over here.”

She got up and walked to him. She was amazed that he could tell what wires were what because they all looked the same to her. He straightened his glasses and picked a wire, holding it between his thumb and forefinger. 

“This one,” he said, “controls the environmental controls in the jumper.” He picked another one while still holding on to the first one. “This is the main power cord that connects all systems. If there’s something wrong with anything, this is the cord that you should check. It’s little bigger than rest.” He pulled another panel off to expose more circuitry. “This is main panel to rerout things.” Carefully, he pulled some wires from where they were connected and mixed them togther, making sure to not mix any open ends. Radek didn’t want to fry himself. “Take these.”

Ali moved and took the wires, separating them with her fingers. She wasn’t sure if he was going to have her start plugging things back in, but she was in no mood to electrocute herself today, and she had the impression that John wouldn’t be too happy, either. 

Slowly, Radek walked her through the process of hooking wires back to where they belonged so she could get the feel of how different connections felt. They did that as many times as it took for Ali to get comfortable reconnecting the wires forwards, backwards, and with her eyes shut. She learned a lot about what sequence connected to which drives and which systems were needed to keep both the ‘Jumper in flight and the crew safe. It was a lot of fun, definitely more hands-on than any of her high school classes, and she was learning something valuable for her new life. Who needed to know the motion of a car when you could learn how to route power to Puddlejumper systems? Radek even taught her how to use the device to measure power output. And when the power wasn’t maximal to the drive circuit, he walked her through rerouting power from another system so that it was. 

“This is soo cool,” she said, replacing the panel that she’d learned to take off. “Thank you so much, Radek.”

“I need four more like you,” he said with a smile, “curious and good listeners.”

Ali beamed at the compliement. And then grimaced when her stomach growled obscenely loud. “Sorry. Time to feed the beast.”

He laughed and looked at his watch. “Yes, well, it almost eight o’clock.”

Her eyes bugged out. “Almost _eight_?” John had said he was going to be back in time for dinner, if everything went okay. Dinner for him was at five, five thirty. That was almost three hours ago! She hurriedly patted her back pocket. Her walki-talkie wasn’t with her; she’d left it on the desk because John was on a mission and because you couldn’t operate from her side to his side without an active wormhole, she’d decided she didn’t need it. She regretted that now and wished cell phones worked. She still carried hers for some absurd reason. 

“Something wrong?”

She was almost panicking. “I – I was supposed to – John was going to be back for dinner and I’m – I’m late,” she helped him pack up the tools that they had been using and carefully, but quickly replaced the last panel. “Thank you so much Radek for teaching me everything today, but I’ve got to run.” She gave him a quick hug that left him speechless and was gone before he could find his voice again.

“You’re welcome,” he said to the empty ‘Jumper.

Ali recalled her track days perfectly as she sprinted through the hallways of Atlantis. John was going to be so mad at her for being late. He was probably tired from being off-world, probably wanted to eat something, shower, and sleep and she was keeping him from what he wanted to do by being late. It was a great way to make an impression on him; the first time he went off-world with her there she couldn’t keep track of time and didn’t tell anybody where she could be found. Well, Radek knew, but that didn’t count. She careened into the cafeteria and stopped. There were a few tables in use, but…John wasn’t in there. 

_Must have missed him. Probably in his room._ She took off like a shot toward the transporter, impatient with the technology, and then jogged down the hall to his door. Technically she was still staying there (John was sleeping on the cot that he’d found in storage) but she had always felt as though it was John’s room, and John’s room only. She tried to ignore the idea that millions of years ago the Ancients had lived in the same city, in the same rooms. That was then, this was now. She opened the door without doing the chime and saw that the room was dark. He wasn’t there, either. She was confused.

_Not in the cafeteria, not in his room,_ she mulled what she knew over in her head. _Doctor Beckett’s?_ It was worth a try. She jogged back to the transporter and tapped the one closest to the where the infirmary was. She refrained from jogging down to the door, instead walking calmly, and opened it. The place was empty except for a sad-looking Marine cradling his left wrist. Ali gave him an encouraging smile, but otherwise didn’t see anybody. It was no use bothering Doctor Beckett for; if John had been in the infirmary, he would have probably been really hurt and Beckett would be out there bustling around and giving orders. Since there was a distinct lack of activity, John hadn’t been through. 

Slowly, she left the infirmary and started the walk back to the control room. According to many in Atlantis, if you had a question about where somebody was at a given moment, Chuck would most likely have your answer. So, she’d ask Chuck. Chuck was also the guy who knew who was off-world and when they were coming back or checking in. John had tried to explain the system to her later that night that he’d told her he was back on full duty and heading out for a mission. 

She smiled when she walked into the control room. The Stargate never failed to make her smile since it was something that was completely unique to the galaxy that she was in. Sure she still felt a pang of longing when she looked at it because of all that she’d given up, but she was starting to think that what she had gained was more precious, more worth it. She wasn’t entirely convinced, but it was getting there. 

Chuck was in his usual seat.

“Hey, Chuck,” she said, hands in her pockets and leaning casually against the part of the console that didn’t have any buttons. “Is John back yet?”

“Not yet,” he said, shaking his head. “He checked in earlier and he’s got about five more minutes before he’s due to check in again. Everything seems to be going okay.” He looked at the tight smile that she gave him. “I’m sure he’d tell you if he was staying the night.” He tried to reassure her. 

“Yeah,” she said, looking over her shoulder at the Stargate. “He’s good like that.” She’d done pretty well stamping down on the anxiety that his first mission away was causing her by spending the day with Radek, but she was beginning to worry. “Five minutes, you said?”

“Three, now,” he said, checking his watch and then screen in front of him. Ali was trying her hardest to not be worried. John did this sort of thing all the time. He was a pro. 

The Stargate began to turn.

“He’s early,” Chuck said, verifying the ID he was getting. The wormhole engaged and Ali watched, one foot tapping anxiously, for them to appear. Ronon was the first through, followed by Teyla and finally, John and Rodney. Ali relaxed instantly and smiled. John was a little late for dinner (unless he routinely ate at eight-something, she didn’t know) but he was still back. He looked up on the balcony, waving when he found her. She waved back.

“I have to go see Carson,” he called, motioning to the rest of his team alredy out the door. She nodded, giving him a thumbs-up, and then turned back to Chuck. 

“I think I got nervous for nothing,” she said, trying to hide the fact that she’d been mildly freaking out that she’d been abandoned by her other parent. She hadn’t known John long, but the two of them were still so new to this, to each other. And when she took a moment, she realized abandoned was too harsh a word to use on her mother. It wasn’t as though she’d wanted to die and leave her with a stranger in another galaxy. 

_But that’s where you are now, so buck up,_ she told herself. “See you later, Chuck.” Leaving before she could embarrass herself further, she walked through the halls of Atlantis on her way to the infirmary. Opening the door she saw each team member on a bed. Ronon and Teyla were in quiet conversation, Rodney was tapping away on his laptop and John was simply sitting there, legs swinging back and forth like a little boy. Honestly, she imagined that’s what she looked like when she’d first seen Doctor Beckett. _Like father, like daughter,_ the little voice in the back of her head wheedled and she hesitated. She took a deep breath and closed the distance between herself and John. He looked up when he heard her coming.

“Hey,” he said. His eyes were tired.

“Hi there,” she said, looking for the plastic chair that was usually beside each bed. Someone must have moved it. It was a little awkward to be standing there, in front of him. Should she ask him to move over?

John sensed her indecision and moved to his left, patting the space he’d vacated with his hand. Ali didn’t hesitate and hopped up to sit next to him. There wasn’t space between them and she found that he was warm. For a few moments the only sound was the tapping of Rodney’s laptop and Carson’s soft Scottish brogue as he talked with Teyla and Ronon. 

“So…what did you do today?” she asked when she couldn’t stand the silence anymore. 

“Ate lunch with some locals and convinced them to trade some food with us,” he said with a shrug, like it wasn’t a big deal. “We brought back some new vegetables for the cafeteria in exchange for helping out with the harvest and finding new irrigation techniques.” He smiled. “It was a pretty good day.”

To Ali, any day that someone helped another was a good day. “That’s cool. I spent the day with Radek.” She smirked and looked over at him as he looked at her. He was doing the one eyebrow thing that she’d seen him give Rodney. “He was working on the Puddlejumpers, which, you haven’t shown me yet and haven’t taught me to fly.” It was childish to guilt-trip him, and she did feel bad when the slight flush crept up his neck, but that was part of Atlantis, too. He’d shown her many things, but he hadn’t shown her what she’d figured out to be near and dear to his heart: things that flew really, _really_ fast. She was living in his world now, the least he could do was share it with her on a more personal level.

“So what did Radek and you do with the Puddlejumpers?” John asked, nudging her gently with his elbow to start her talking again.

“Oh,” she said, slightly startled. “He taught me how to tell differen wires apart, like which ones went where and what they controlled. He taught me how to route power in case the power output wasn’t enough to certain systems.” She grinned, genuinely happy. “It was really fun.”

John smiled, sharing her happiness. It sounded as though she’d had a blast with Radek for the day and he made himself a mental note to ensure that when she did something, she could be hands on with it, learn from it. When he took a moment and thought about it, how her life had changed, he realized that college wasn’t really an option for her anymore. Atlantis and the Pegasus Galaxy would have to be her school, its people her teachers. And as long as the Wraith stayed off the tenure list, he wouldn’t really have anything to worry about. 

“So you like the ‘Jumpers?” he asked, rolling up his sleeve as Carson approached. 

She smiled in greeting to the Scottish doctor and said, “They look like a lot of fun. I mean, I only saw the inside of one when it wasn’t on, but Radek says that because I have the gene it’s like turning on a life signs detector, only with a little more finesse.”

“Puddlejumpers,” Carson said with a slight shiver. He wasn’t really comfortable with operating anything bigger than a medical scanner since what had happened in Antarctica when he’d nearly shot General O’Neill and Sheppard out of the sky by accident. Then there was when John had thought it would be a good idea to teach Carson and Rodney to fly at the same time. Talk about needing the inertial dampeners that day.

“Oh, come on, Carson,” John said with a grin. “You know you love them.”

“They’re fine ta be in, but not to drive,” the doctor said, snapping his gloves on and picking up a needle from the tray beside him. He looked at Ali and stage-whispered, “They fly with the grace of a bumblebee and go very, very fast. That’s why he loves them.” 

Ali giggled. Carson took his required blood sample from John’s arm, applied a piece of gauze, and blatently ignored the frown that John was giving him for the dig on his beloved Puddlejumper. With one last grin, Carson stripped his gloves off and handed the sample to a nurse, on his way to Rodney. 

Hopping down from the bed, John rolled his sleeve down and gave Ali a hand. “Tell you what,” he said as they headed for the door to the infirmary, “I have to be in debriefing and meetings all day tomorrow, but the day after, that’s when you and I’ll go.”

“Go where?”

“The mainland.” He looked at her. “I’ll teach you how to fly.” The joy in her eyes was well worth the six words it took to put it there, even though he was sure he was going to be very glad of the inertial dampeners in the ‘Jumper. _She’s a Sheppard. She’ll take to flying like a duck to water,_ was the reassuring thought in the back of his head. Hopefully it would stay there.


	3. Integration: Learning to Fly

**Summary for the Chapter:**

> John's a pilot with a love of things that fly stupidly fast, and he hopes Ali shares that same love. 
> 
> Or: Learning to fly a puddlejumper might be an unmitigated disaster instead of a father-daughter bonding experience.

After spending the previous day locked in meetings and debriefings of almost every team that had been off-world and had come back on the same day, John was more than ready for a break. His brain was oozing out of his ears from all the reports he was going to have to go through. Then again, that’s why he had Lorne. 

“You’re in charge while I’m gone and no, no idea when I’m going to be back,” John said upon entering his XO’s hole in the wall office. Lorne looked up from the stack of paperwork he was working on.

“Okay,” Lorne said slowly, drawing the word out. “Anything I should know about?”

“John!”

Lorne craned his neck to look past Sheppard to see Alison standing in the doorway, backpack on her back and a grin on her face, excitement shining in her eyes. 

“I’m coming, I’m coming,” John said, a smile on his face as he tried to placate her. He turned back to Lorne. “I’m heading to the mainland.”

“He’s teaching me to fly,” Ali called from the hall. “Just so you know.”

John turned a little pink. “I’m teaching her to fly, and speaking of that, we’re a little late – ”

“ – Because somebody wouldn’t get up this morning!”

Lorne stifled a grin. “I got it, sir. Have fun.” He waited until Sheppard was gone before chuckling to himself. He hadn’t seen Sheppard that relaxed in a while, really ready to just have a day to himself and have a little fun. Then again, he could see Alison hitting golf balls off the south pier as he easily as he could see Teyla, but still, that wasn’t the point. Still grinning, he went back to his paperwork.

 

Ali settled herself into the co-pilot’s seat like it was her job. She couldn’t help the permanent smile that was plastered to her face; she was both happy and nervous. Happy that she was going to learn to fly a _Puddlejumper_ in _Atlantis_ and it would be her first time flying _anything_ , but also nervous because she was spending her entire day with John. There were still awkward silences between the two of them sometimes, especially during meals, but they were getting better. This would be an interesting test of just how far they’d come in a short period of time. Ali wasn’t sure how she could track their improvement. 

“Okay,” John said, sliding into the pilot’s seat with ease. From her point of view, it looked as though he truly belonged there and she realized how close flying was to his heart. He looked at her. “I want you to close yours eyes and don’t open them until I tell you. And _no_ peeking.”

More than a little confused, she did what he asked and closed her eyes, settling back against the seat. Because she had her eyes shut, her other senses picked up the slack. She could feel the thrum of the ‘Jumper underneath her as John fired it up. There was a moment when her stomach dropped as they rose, but it wasn’t anything like what she had experienced on an airplane, and she was pressed back into the seat padding as the ‘Jumper moved forward. She wanted to open her eyes…

“Keep ‘em closed,” John said, smiling. He took the ‘Jumper up above the city, angling so that the sun was partially behind the central tower and the water sparkled. It was a gorgeous panoramic view. “Okay, open ‘em.”

Ali opened her eyes and gasped in awe and wonder at what was before her. She leaned forward, both hands carefully on the panel in front of her, eyes wide as she tried to commit the beautiful sight to memory. It was the most stunning, beautiful thing that she had ever seen in her life. She was speechless.

“Beautiful, isn’t it?” John asked with a grin. 

Ali’s mouth moved but nothing came out. When she found her voice, it was breathless, “It’s amazing.” She leaned back against the seat and looked over at him. “It’s gorgeous.”

He beamed. “Yup.” He started the ‘Jumper away from the city, headed toward the mainland and turned on the autopilot. “Now it’s time for the next part of the day.”

Ali felt the butterflies in her stomach return. “The flying?”

“Well, you are flying now, technically speaking, but yeah, the flying,” he said, getting out of the pilot’s seat. She slithered out of the co-pilot’s chair and stood nervously next to the other chair. John sat in the co-pilot chair and motioned for her to take a seat. She sat gingerly, not sure what to do. “Okay, now this is a bit like using a life signs detector with that it takes mostly the gene to keep it going. So put your hands on the controls and just get a feel for it. Feel it in your mind.”

She put her hands on the controls, pleased when they didn’t shake. She could feel the ‘Jumper like she’d started to feel Atlantis, a hum in the back of her mind. “Okay.” 

“I’m going to take the autopilot off.”

Ali could feel the difference when he did that and she thought hard, _Stay on the course that he had_ and sure enough there wasn’t any real deviation in the path of the ‘Jumper. She spared one brief glance at him and saw that he was leaning back comfortably in his chair, arms over his chest with a self-satisfied smirk on his face. That was when she realized that she was flying the ‘Jumper all by herself. It really was almost like second-nature. 

_She’s a Sheppard,_ John thought with pride. 

The silence stretched but it wasn’t uncomfortable. “Does this thing have a radio?”

She should have known that he had a list of Johnny Cash tunes because that was what started playing through the speakers. She laughed.

 

“Okay, now this part can be a little tricky,” he said after about half an hour of flying. The mainland had come into sight. “Head over in that direction.” He pointed to her left through the window and she obligingly steered the ‘Jumper in that direction. A few minutes later a spacious beach came into view, sand a plenty and enough space for even a rookie to land a Puddlejumper. “Just ease it down gently,” he said, hoping that his calm voice would help her nerves. He could see that her hands were a little shaky. 

“Like this?” she kept a firm hold on what she wanted the ‘Jumper to do, both excited and scared that John had thought her good enough to land them without killing them both or horribly mangling the ‘Jumper in the process. 

“You’re doing fine,” he said. 

She managed the maneuvre the ‘Jumper so that it was over a wide, bare patch of beach. She got it down to about twenty feet above the sand and then stalled. Biting her lip, she let it go and the ‘Jumper dropped the rest of the distance, landing with a _thump_ , sand flying everywhere upon impact. She winced and looked over at John who was clutching the seat to keep himself upright. 

“You did better than Rodney,” he said, and with that the tension leaked immediately from the silence. She grinned. 

“Thanks,” she said, letting go of the controls and heading for the back of the ‘Jumper. It was a compliment from him, something that she’d thought wouldn’t come for a long time. 

If someone had told Ali that she would travel to another galaxy to live with her father, learn how to fly a “Puddlejumper,” and then spend the next four hours of her life building a sandcastle with John she would have said that person was absolutely crazy. But there she was, building a horrendous sand sculpture with John and laughing at his not-so-funny jokes and not caring that they weren’t funny. It was as though time had stopped for them, holding them in the moment when it didn’t matter that they’d only known each other for a short period of time. Ali had felt that happy and carefree in a long time, and she could tell from the way John’s eyes were sparkling with laughter that he hadn’t either. She’d once heard it said somewhere that laughter was the best medicine and could add years to your life.

“Do you know that laughter can add years to your life?” she said, a little randomly, scooping sand into a mound.

“Yeah?” he asked, genuinely interested. 

“Yeah,” she grinned. “I forget how many years it adds to your life, but it adds quite a few.”

John took a moment to look deep in thought which brought an anticipated grin to Ali’s face. “So, I’ve put on about ten years, give or take?”

She laughed, free and easy, and nodded. “Sure. If you wanna look at it like that, go ahead.” 

He figured that was what people meant when they said to look on the brighter side of life. Adding years to your life was something that he wouldn’t have thought he’d be doing in the Pegasus Galaxy with the threat of the Wraith to suck it out of him. He took a moment to remind himself that the threat was always out there, that it was a gamble every time he stepped through the ‘Gate as to whether he would come back in one piece or come back at all. That, and Ali had no idea what in hell a Wraith was. And John intended to keep it that way for a good, long time.

“You okay?”

John looked at Ali over the mound of sand slightly resembling a castle between them. “Yeah. Just…Just got a little lost in thought. All the paperwork I’m making Lorne do.” He gave her a smile but it didn’t reach his eyes all the way as his previous ones had. As Ali didn’t seem to notice the difference, John didn’t comment, and it would certainly make things interesting.


	4. Integration: Metamorphosis

**Summary for the Chapter:**

> A remix of _Metamorphosis_.

**Notes for the Chapter:**

> I did take some dialogue right from the episode (and totally failed to mark which I took and which I didn't, damn it) and the lines at the end are from Jules Verne's _Journey to the Center of the Earth_ which is one of my favorites.

Ali was slowly finding a rhythm. She had self-defense lessons with Teyla twice a week, spent a bit of time with Radek every day learning something new, and always had lunch with John at one. She watched movies with Ronon and taught him more Earth culture (and learned a little more about Sateda, too) and sometimes sat on an empty stool when Rodney used John shamelessly as the equivalent of a light switch. She didn’t see too much of Carson because he was usually in his lab working on something or in the infirmary, taking care of people. She’d been near the infirmary, just walking the route that John and Ronon ran in the morning, when Major Lorne came around the corner leading a dazed-looking Parrish. He gave her a brief wave then surrendered Parrish over to the Scot. Carson gave her a brief smile and helped Lorne lead Parrish to an exam bed. Ali had continued on her merry way. 

Some afternoons, after lunch with John, she’d find a balcony and just watch the waves lap gently against the city. It was a soothing sound and it allowed her to sort through all that was going on in her life, how it had drastically changed. Atlantis was becoming home to her now, its people her family. Radek and Rodney had been phasing her out of calling them “Doctor Zelenka” or “Doctor McKay” and by their first names, but it was strange for her. She wasn’t used to calling adults by their first names, especially not ones who were so much older and had multiple degrees under their belts. Everything was slowly becoming routine for her with the exception of one very large fact of life that was simply unavoidable: John’s off-world missions. It wasn’t that she wasn’t used to being on her own (her mother had worked for the government and could be gone for days at a time, leaving her alone when she was old enough) but it was the nagging voice in her head that said there might be a time when John _didn’t_ come back through the ‘Gate.

_Everybody deals with that every day,_ she argued with herself. _It’s what they signed on for._ Still, it didn’t make it any easier to bear. 

Regardless of how she felt, she found herself on the balcony overlooking the Stargate as John and his team prepared to head out. She leaned against the railing, watching the way that the team interacted. She knew they were close, more like family with all that they’d been through, and she also knew if she gave them the chance, they could be her family, too. It was still hard. She still missed her mother, all of her old friends. Most of all she missed Earth.

She shoved those thoughts to the back of her head as the wormhole engaged and she stood up. She couldn’t help but think of what the people below her were thinking when they made the choice to leave their homes on Earth, and come to Atlantis. Had they wanted to leave? Or had they wanted to stay? The impression she got from some was that, though it had originally been a one-way trip, they’d been more than excited to go. John included. Which kind of rubbed her the wrong way when she thought about it.

John looked up at her and waved, giving her a smile. She waved back and watched as they disappeared into the puddle. When it disengaged, she looked at Chuck and gave him a small smile. She needed a hobby. Badly. Or something to distract her from all the thoughts in her head. She rubbed her hands together and looked around at all the people at their consoles. It was then that she was hit with a pang of uselessness. Everyone else was there for a reason, had a job to do. She was simply there because her mother had left it in her will, and the higher-ups had approved. She had no purpose on Atlantis other than to take up space and be looked after by John. And Rodney. And Radek. And the rest of Atlantis, really. 

_I_ really _need a hobby._ She waved a goodbye to Chuck and wandered away, through the consoles and out into the hallway. She took her time, stopping in the cafeteria for a bottle of water. She wandered down past John’s hole-in-the-wall office and, in the same hallway only further down, wandered past the open door to Lorne’s. She paused and then poked her head cautiously around the doorframe. Lorne was bent over a pile of paperwork, pen in hand, and totally focused.

“Hey, Ali.”

She jumped nearly a foot in the air. Apparently he wasn’t so focused as she’d thought, or he just had the ability to realize when people were staring at him for no good reason. _Or, maybe it’s because he’s a soldier. You’re such a moron._ The voice in her head was chastising her again but she shoved it aside, as usual. “Sorry. Didn’t mean to disturb you.”

He looked up from his paperwork. “You’re not disturbing at all. If it was your dad, then, well, I’d think he was up to something.”

She pressed her lips together in a tight line and smiled a bit. It only served as a reminder to her of the distance still between her and John when someone else referred to him to him in conversation as “your dad” or “your father.” He was still John to her. She didn’t know him well enough yet to call him something that close and loving. It wasn’t a matter of whether or not she loved him, she did, really, deep down because he was her father, but she didn’t know him yet. They didn’t have the typical relationship that everyone else had. She knew him as John. And John was what he was going to be to her until she felt she knew him well enough to call him something different. She wasn’t sure the rest of Atlantis would be on the same page as her with that, so she smiled and accepted it whenever anyone else made the reference.

“He would probably be up to something,” she agreed amicably. From what she was gathering about John, most of the time he was up to something or other. “Paperwork?” It was obvious, but she felt the need to ask anyway, to keep the conversation going.

“Yup,” he said. “Lots of it, too.” He sat back in his chair. “How were your flying lessons?”

“They were _so_ much fun,” she said with a grin, eyes lighting up immediately. She stepped into the office, moved a pile of papers and folders from the only chair in the room other than the one Lorne was occupying, and sat herself down. “Those ‘Jumpers are the coolest thing I have ever seen. And the view over Atlantis was amazing.” 

“Atlantis sure is beautiful,” he said. He reached out for the folders in her hands and she handed them over, still rambling about the view from the air and about how fast the ‘Jumpers went and about how much _fun_ it had been to just spend a day with John. Lorne couldn’t help but smile. He let her talk herself out, casually glancing at the report in front of him while still listening and making appropriate listening noises. He looked completely at her when she was silent for more than ten seconds.

Ali was looking at the pictures on the wall behind him, the ones of the central tower in Atlantis. One was in paint, the other in charcoal or pencil, but both were absolutely fantastic and of great skill. “Those are awesome.”

Lorne blushed faintly. He sometimes still had problems taking praise without turning pink. “Thank you.”

Her hazel eyes snapped to his gray ones. “Those are yours? You drew them?”

“Drawing’s a hobby of mine,” he said. “I do it in my spare time.”

“Wish I could draw like that,” she said wistfully. The she remembered that they had talked about his painting hobby, back when she’d first arrived in Atlantis. That seemed like so long ago, such a foreign time for her. It made her wish she had a hobby of any sort. “I mangle stick figures.” It was only a slight exaggeration.

“Oh,” he said, nodding his head, “that can be very…interesting.” He smirked. 

“Yeah.” She knew he wasn’t laughing at her, but smirking at the idea that she thought she couldn’t even draw stick figures. 

“If you wanted to, on my next day off, which is in about two weeks or so, I can teach you to paint,” he said. “From what I heard from Radek, you’re pretty easy to teach.”

Ali blushed pink at the praise from him, but especially Radek. She still remembered that day in the ‘Jumper and had made a point to just drop in on him randomly, to see if he needed help with anything. That had led to some interesting experiments, but most of the time it allowed her to spend time as the “Mini Lamplighter” and helped her further learn to use her gene. And it wasn’t like she had anything else going on during her days that would prevent her learning to paint from Lorne. 

“Sure,” she said. “Hope you’re a good teacher.” She stood; she should let him get back to his paperwork. He, unlike her, actually had a job to do. “Just, um, send me an e-mail.” She grinned. She had only just had an e-mail address set up recently and it was kind of fun. It made her feel like she was part of Atlantis.

“I can do that,” he said, shuffling the file folder he had been looking at to another part of his desk. “Have a good day.”

“You too. Oh, how’s Parrish?”

“David’s doing alright. Broke his arm, though. He’ll be in a cast for a little while and won’t be able to go off-world. But he’s good.” Lorne smiled at her, pleasantly surprised that she’d asked about the well-being of one of his teammates. 

“Cool. Maybe I’ll stop by and sign his cast or something. See you later.” She gave him one last smile and then left his office. She resumed her walking, stopping every now and then just to look at the beautiful stained-glass windows. Atlantis was simply beautiful. 

_I wish mom could see this,_ she thought and sighed. She turned and made her way back to the room that she was still sharing with John. She was beginning to feel guilty that he was still sleeping on a cot while she had the bed. What she really needed was her own room. Maybe when he came back she could talk him into helping her move into one of her own. It didn’t have to be far away from his – she wasn’t sure about that, and she knew that he wouldn’t be thrilled about it, either, but she really wanted her own space. Needed to have her own space, really. She could probably find an empty room, not too far from his, and have her stuff moved there by the time that he got back, but that wouldn’t be fair to him. He would have wanted to help her move, help her get settled. It was a dad-thing. And whether she really liked it or not, she _was_ his little girl. Some days that was debatable, but she had no desire to do anything to rock the boat on their still-developing relationship. 

To occupy the time, she grabbed the book she was borrowing from Elizabeth and dragged the chair from the desk out onto the balcony. There was a light breeze, but otherwise the day was perfect. Clouds floated across the sky but it was beautiful. She settled into the chair, propped her feet on the balcony railing and settled in to burn a few hours immersed in the world of Jane Austen.

* * *

Ali was heading for the cafeteria for a snack when she heard the commotion. She looked behind her just in time to see the gurney heading for the infirmary, and to see that John was the one on it. Snack forgotten, she changed course immediately and headed after it.

“John?” she called, jogging to catch up.

”This really isn’t necessary, Doc,” John said as he was wheeled into a room.

”Yes it is, you’ve got a serious laceration on your arm and lost a good deal of blood,” Carson informed him, not batting an eye as John tried to weasel his way out of medical attention. 

Ali entered the room right behind them, standing well back out of the way, but still there. “John?”

John looked up from the gurney. “Hey, Ali. I’m fine.” It was an automatic response despite the looks he got from all the nurses, Carson, and his own daughter. “Really.”

_Doesn’t look like “fine,”_ she thought, but kept her mouth shut. From behind her Rodney was complaining about something, a splinter by the sounds of it. She didn’t turn around to see; she was too focused on John and the commotion he’d brought with him.

“All right, let’s have a look at this,” Carson said, unwinding the bandage around John’s arm. He took a swab from a nurse. “This may hurt a wee bit.” Ali flinched in anticipation as he started swabbing down John’s arm. She’d been on the receiving end of that treatment before and it wasn’t fun. Rodney made enough noise from his splinter for the pair of them. 

”This doesn’t sting?”

John looked at the doctor. “No.” He looked over at a pale Ali.

“I know you have a high threshold for pain but this is - ”

“This is what?” John alternated between looking at Carson and Ali. He was almost tempted to have somebody make her sit down by the look of it, but her eyes said a different story. There were quite a few stunned and surprised faces when the doctor announced that the “feeding mark” was gone. Ali was confused but shoved it to the back of her mind because John was all right. Apparently. She allowed herself to be herded outside the room while Carson talked privately to John, and stood there, absently chewing on her fingernails. It was a nervous habit that she could have sworn she got over years ago, but decidedly made a comeback. It happened mostly when she was stressed. She shoved both hands in her pockets when the door opened and he stepped out. 

“I’m fine,” he said, showing her his arm for further proof. There wasn’t anything there that she could see. “He said to just go about my day.”

She didn’t know what to say to that. And then she remembered what she had been thinking earlier. “Hey, John?”

“Hey what?” He started walking toward the cafeteria, unconsciously matching his pace to hers. It was something they’d started doing naturally when walking together. 

“I want to move out.” She looked up at him and laughed at the look on his face. “Not like that, but I want to move out of your room. I’d like one of my own.” She gave him her best, most endearing smile and the “puppy-dog eyes.” 

“You know,” he said, “I was actually thinking the same thing.” It had been in the back of his mind, but the smile he got from her made him glad that he’d essentially agreed to it. 

As it turned out there was an unoccupied room only two doors down from John’s. After grabbing a sandwich from the cafeteria, they spent the rest of the afternoon moving her things from one room to the other. Ali put the sheets she’d brought with her from home on the bed, while John cursed his way through setting up the laptop on the desk until everything was the way that she wanted it. Now it felt more like home. Not that John’s room hadn’t before, but this was something that was uniquely hers. Her own space. Somewhere she could retreat to when she was having a bad day or just needed some time on her own. And, John could go back to sleeping in his own bed instead of the back-breaking cot that he’d spent the last few weeks tossing and turning on. And Ali could feel better that she wasn’t taking up someone else’s space anymore. 

“Thanks, John,” she said, sitting crossed-legged on the bed while he sat in the desk chair. It really wasn’t much, but it was something to her. Something that made Atlantis a little more like home. 

“No problem,” he said. That was when he got the call from Carson to come to infirmary. From the stress he could hear in the doctor’s voice, it probably wasn’t good. A quick glance at Ali told him that she could read him just as easily as he could her, and he knew sooner or later he would have to tell her about what he’d hoped to keep from her as long as possible: the Wraith. “That’s the Doc.”

“Yeah?” She could tell something was up, something big. He got up to leave and she followed. “I’m coming, too.” There was hesitation in her voice but she straightened her spine. What effected him now effected her, and the other way around. It was one of those things they were still getting used to.

When they got to the infirmary, she was more than a little surprised to see Elizabeth in the room as well. Carson was seated at a desk, while John hopped on the exam bed. She leaned against the wall and tried to be as inconspicuous as possible. Still, she couldn’t help but feel her pulse quicken. Carson’s initial statement didn’t make sense to her, but she let it go. That wasn’t the important part. Since John didn’t seem to think that was a big deal, she was willing to go with the flow. Carson’s next words confused her even more but she caught the gist of it, questions rattling around in her head all the same. John had been infected with a virus? A virus that was supposed to make somebody a human? Weren’t all people in the Pegasus Galaxy human to begin with? Ali had nearly a million questions ratcheting around the inside of her brain and tried valiantly to stay as focused as possible to the conversation around John’s well-being. The one thing that jogged her memory was the mention of the Iratus bug. John had mentioned it in a story about one of his missions-gone-pear-shaped when she’d first arrived. But what Carson was saying was that John was going to turn into a bug..which didn’t sound _possible_. Then again, the lost city of Atlantis didn’t sound possible either, and she was currently taking up residence there. Anything was possible, apparently. Hell, maybe pigs flew in this galaxy. 

_There’s that word again. Wraith._ Ali thought, her eyes focusing on Elizabeth. Elizabeth was the one person that she’d become accustomed to calling by her first name from the moment she’d touched down from the _Daedalus._ Ali borrowed books from her now and then. She felt worry curl in her belly when Carson, usually unflappable Carson, had no idea how the drug was going to react with John’s system. She wanted to question him, demand he know what to do, but bit her lip to keep her mouth shut. They had enough to worry about; they didn’t need her freaking out on top of it. She’d been tuning out the conversation and listened back in just in time to hear John say, “She was spitting an awful lot.” 

From the look on Carson’s face, he didn’t find the remark nearly as humorous as she did. She barely kept the smirk off her face. Ali took a look at her shoes to make her face blank again, and felt a little happiness blossom in her chest that John wasn’t going to be able to go off-world while this was going on.

“See you in six hours,” John said, hopping off the bed. He held his hand to Ali. “Dinner?”

“Sure,” she said. She took his hand and away they went.

* * *

There were so many questions still buzzing around in Ali’s head, but she didn’t know where to start. She sat on her bed and tried to make sense of the conversations that she’d heard, the information she’d gathered, but it really wasn’t making any sense. Then she had an idea. She was connected to the network now, so maybe she had use of the databases that the scientists had. She uncurled herself and reached for her computer. Out of curiosity, she flipped open the laptop and tried to access one of the databases. She tried her new username, and the password and hit enter.

**Access Denied**

_Okay, then,_ she thought. _Maybe it’s having issues._ She tried again, and got the same result. _Third time’s the charm. Always._ Nothing. Frustrated, she closed the laptop with a sharp click. There really was no other way around it. She was going to have to ask John for some answers. Whether or not he would answer was one thing, and whether he would answer truthfully was quite another. She put her sneakers back on and headed out of her room and down the hall. That’s where John had told her he was going to be until his check-in with Beckett. She waved her hand over the chime and waited. And waited. She did the chime again. Even if he was sleeping, John was a light enough sleeper (being in the military had done that to him) that he was usually awake with the first chime and at the door before the person outside could even think of doing it a second time. 

She pulled the radio from her back pocket. It was habit now that whenever she left her room, she took it with her. “Ali Sheppard to John Sheppard.” She waited but he didn’t answer her. 

_Maybe something went wrong,_ the nasty voice in the back of her head whispered to her. _Maybe something went wrong and he’s not as “fine” as he’d like you to think he is. You might lose another parent._

“Shut up,” she whispered, and stuffed the radio back into her back pocket. She forced herself to walk calmly to the transporter and pick her destination. From there she, again, forced herself to walk to the infirmary. She got there in time to see the worry on Elizabeth’s face as Carson delivered what was obviously bad news and had never felt so completely in the dark as she did then. 

“How long do we have?” Elizabeth asked.

“What?” Ali said, finding her voice from near her stomach where it had sank. “What do you mean…how…what do you mean how much time do we have? What is going on?” She looked between Carson and Elizabeth, waiting for an answer. Better yet, an explanation would be fabulous.

“I’m not sure, exactly,” Carson said, looking not at Ali but at Elizabeth. 

Ali rolled her eyes and tried very hard not to let her temper get the best of her. She was getting tired of being overlooked. When she had herself under control enough to listen again, and heard Carson speak of days, she had to fight the urge to throw up. John had _days_ left? Had she moved to another galaxy, away from the death of one parent, only to lose the other?

“Wait. Wait. Wait!” she said, stepping between Carson and Elizabeth and holding her hands up. “I understand that this is probably something very strange and very dangerous, but you just said John had _days._ Will somebody _please_ tell me what the hell is going on?” She didn’t mean to let the curse slip, but it did. She was upset. That was understandable, right? She wouldn’t somehow be grounded for this when John was all right again, right? Because he _would_ be all right again. 

Carson stood up. “You might want to sit down.” The way he said it wasn’t a question, it was a statement. Ali sat in the chair. “A retrovirus has been introduced to Colonel Sheppard’s body and instead of being broken down like we had hoped, it’s changing his DNA into something close to that of the Iratus bug.”

“The thing that attached itself to his neck like, a year ago?” Ali asked. She wanted no holes in her knowledge.

“Aye.” Carson must have thought that was a suitable explanation because he looked at Elizabeth.

“What’s the plan?”

Ali watched the proverbial game of tennis between the two, her heart sinking to her knees when Carson said he didn’t have a plan. She looked up at him, the determined look in his blue eyes telling her that he would do everything in his power to make John better, to fix whatever had gone wrong. She sat in the chair, pulling her legs up and wrapping her arms around them as Elizabeth went to talk to John. Carson said nothing further, heading back into his office to continue working on a cure and leaving Ali with all the thoughts in the world in her head, first and foremost being whether or not she was going to be an orphan very, very soon.

* * *

John was preparing to do something decidedly relaxing to take his mind off the fact that he was mutating into a bug, when the chime on his door sounded. “Come in.” He stretched out, looking up to find Ali standing at the foot of his bed.

“Hey.” Her voice was small, guarded. She worried her bottom lip between her teeth. “How are you?”

“I’m fine,” he said, sitting up and patting the space next to him. She took the seat without hesitating, a sign of how improved things were between the two of them. He looked at her pale face and wide eyes and realized that she wasn’t doing too well herself. When he thought about it, he probably wouldn’t be all right with the idea of losing someone, let alone a second someone in less than six months. And then there was the manner of what was going on with him, the fact that he was essentially mutating into a bug, a bug that had connections with the Wraith. 

Speaking of the Wraith, he’d seen her and Carson talking. Just how much at the good Scottish doctor told her?

“You know what’s going on?” he asked. 

“Sort of.” She was frustrated with the lack of information she’d been receiving, the incomplete picture she still had. She bumped his shoulder with hers and stayed there, leaning against him. She was so afraid of losing him, so afraid of being alone. “Carson explained a little of it.”

John let out a sigh of relief. “Tell me.”

Ali looked at him sharply. He wanted her to tell him what was going on with his body? Shouldn’t it be the other way around? “Well, Carson said that you were infected with a virus, one that wasn’t meant for humans. Basically, you’re turning into a bug.” Her voice cracked a little on the last part and he awkwardly slipped at arm around her shoulder. He wasn’t a big fan of hugs, had never been, but with her he found himself showing more physical affection than he had with anyone, including her mother. He felt she needed it and he was more than willing to try. 

“That’s basically it.” He gave her a quick squeeze and then released her. 

“Can I see where she bit you?”

John was taken aback by the question but since there was no lasting damage it couldn’t hurt. He extended his arm to Ali and she touched his forearm, inspecting it. He shivered as she brushed a fingertip over a sensitive patch of skin by the crease of his elbow. 

“Huh.” She looked up at him. “Do you have psoriasis?” 

“What?”

“Your skin, it’s scaly. I had a friend back home who had this skin condition, well, immune system thing really because her body thought it needed to fight something that wasn’t there and her skin got kind of dry and scaly and I’m just wondering if you have that.” She bent her head closer to his arm. “But Sally’s wasn’t blue.”

John took his arm back and looked at the spot she was talking about. It was indeed scaly, right over the spot that Elia had fed from him. He poked it. Steadfastly avoiding Ali’s gaze, he put his radio back in his ear and said, “Hey doc. We might have to move that first check in up.”

“That’s not psoriasis, is it?” It was probably the stupidest thing she’d ever said, and Ali found she didn’t care. She was steadfastly hoping for a yes, but she got what she knew was coming.

“No, Alison, it’s not.”

* * 

Elizabeth hadn’t been expecting to see John Sheppard strolling toward her office, required guard in tow, along with Ali. Ali looked tired; there were circles under her eyes.

“Look! I made a new friend.” John grinned at her. 

Ali smiled, leaning against an unoccupied console while John was in with Elizabeth. This was the way that she could spend time with John, sometimes following him around the city, always _behind_ the security detail as he had instructed. She took a deep breath and looked over the hustle and bustle of Atlantis, people from all different countries and walks of life working together. She was doing anything and everything she could to keep her mind off the fact that John was mutating into something and she was, for all intents and purposes, powerless to stop it. As it were, she was completely unprepared for the sound of breaking glass behind her, from Elizabeth’s office. John was looking a combination of frustrated and embarrassed and Elizabeth’s face was stony.

_That’s not good._ She missed John’s obviously semi-flippant response and watched Elizabeth’s face harden further. _Really not good._

* * *

John had stopped letting her inside.

In order to spend time in his presence (if you counted attempting to talk through a door with a security detail standing literally over your shoulder) Ali had been forced to sit outside John’s door. The radio sat on the floor beside her, quiet and forlorn. John had either taken his earpiece out or was refusing to talk to her. She didn’t want to think about what was happening to his psyche, the balance that he was teetering with, whether or not his mind was turning into a bug at a faster or slower rate than his body. She didn’t want to think of how rough the blue iridescent scales on his arms and neck looked, or how pretty, despite what it was doing to him. In what she supposed was true John Sheppard fashion, he was closing everyone he felt close to out, though what he really needed was to have them close. He was closing her out when she really needed him to sit next to her and tell her everything was going to be okay. She needed all the reassurance she could get, though she still didn’t have all the details and the master plan was fuzzy at best. 

Ali drew her knees to her chest and pressed her cheek against the soft denim of her blue jeans. She wasn’t a member of the expedition and even if she had been, she still would have wearing those jeans. They were her lucky ones, the ones she had worn for every math test, the day of every track meet. She’d read the fiction books about pants, too, about the four best friends who’s pants magically fit each of them. She wasn’t hoping for a literature-inspired miracle, she was just hoping for some luck and a ray of sunshine on a cloudy day. 

“Hi, Ali.”

She looked up at Elizabeth and felt her heart sink. As much as Ali liked the woman, respected her, Elizabeth was no ray of sunshine. Not when it came to John and the entire bug situation as a whole. Ali smiled thinly and went back to staring at the floor, her cheeks pressed against her knee. 

The guard looked at Elizabeth. “I wouldn’t go in there.”

_Yeah, today’s not one of John’s better days._ Ali traced a random pattern on the tile, listening to the door open and then shut. She looked up at the young Marine. “Not one of his better days, huh?”

“Nope.”

Everyone had good days and bad days. Lately, John’s were becoming more and more…not-so-fun. Ali couldn’t blame him. She’d probably be completely freaking out if she were in his position but she wanted to thump her head against the wall every time he would ignore her. He wasn’t on his own anymore, damn it. He couldn’t just die and fade quietly away. He’d leave Ali behind if he did. 

The door hissed open and she might have assumed Elizabeth was coming out if it hadn’t been for the scuffle. Ali flinched against the wall when the guard hit the floor, out cold from the look of it. She scrambled to her feet and across the hallway, putting herself in front of John so she wouldn’t sneak up on him. She had a feeling sneaking up on him – even accidentally – would be very, very bad. 

His yellow cat-like eyes locked on her hazel ones and she froze. He took a step toward her and, with her heart thumping madly against her ribcage, took a step away from the wall. John might not be in complete control anymore, but Ali was dead certain with every fiber in her being, that he wouldn’t hurt her. She was his daughter. He wouldn’t hurt her.

“Hey.” She kept her eyes on his, not straying to look at the blue scales that covered most of his visible skin. There was something about the eyes that spoke to her; though they were a different color, they were still John’s eyes. They still had that look that was invariably John Sheppard. 

He cocked his head to the side and took another step toward her. She smiled thinly and stepped toward him again. She stayed still and allowed him to close the distance to her. Her eyes stayed on his the entire time, even when he reached up a clawed blue hand to very gently move a strand of her hair away from her jawbone. Ali knew the John she knew was still in there somewhere, still holding on, waiting for Beckett to find an answer. 

“John,” she murmured as his hand returned to his side. She reached for it in midflight, not surprised when he flinched away from her. He looked at her one last time, turned, and ran down the hall. Elizabeth appeared in the doorway seconds later, calling in his escape. Ali stood stock-still in the hallway. He was still in there somewhere, waiting to come back.

* * *

Ali didn’t care that he’d been stunned by Ronon. It was probably the only way they would have caught him without doing him damage. Ali had an immediate fierce protectiveness in her chest for John when it came to Caldwell, all gratuity aside that he’d ferried her across two galaxies, putting up with her silence and cold shoulder while she was dealing with a ton of emotional baggage at the time, and it really hadn’t helped that he’d basically said “shoot him” in order to bring John back in. Caldwell was not at the top of her Favorite People List.

Neither was Carson Beckett. 

“I want to see him,” Ali said, looking up at Carson with as much force as he was looking down at her. Beyond him was John motionless in a medical bed, restrained. 

“Lass, he’s in a medical induced coma at the moment,” Carson said, his reasonable tone making her more on edge. 

“Okay, so he’s not going anywhere and he’s not awake. Why can’t I see him?”

Elizabeth appeared over his shoulder. “We’re not sure it’s the best idea at the moment.”

Ali looked from Carson to Elizabeth. Took a deep breath and slowly started to count to ten. All of her frustration was bound to come out eventually and it wouldn’t help to take either one of their heads off, even if inadvertently. Carson had sharp needles at his disposal. But they just didn’t get it, did they? They just didn’t understand that Ali wasn’t just worried about John’s mental and physical health. They didn’t understand that this was difficult for her, too, to possibly lose a good friend. They didn’t understand what it was like to be hanging on the edge of losing _another_ parent. 

“I understand that you two are worried,” Ali said, mustering up calmness from somewhere, “that you have my safety, and John’s, in mind. But like you said, he’s in a medical induced coma right now, and restrained, and he’s just there.” She worked her jaw back and forth, tears coming from nowhere. “I’ve…I’ve already lost one parent in my life, and let’s face it, I might lose another.” Her gaze dared Elizabeth to say something to the contrary, something stupid and designed to make her feel better without any real weight behind it. The woman looked ready to do so; Carson stayed quiet. “I might lose another. He will not hurt me, even if he somehow wakes up, and gets out of those restraints, he will not hurt me. I know this because I’m his daughter. And I just want to go see him. Please.”

Carson stepped out of the doorway and Ali didn’t hesitate, didn’t even say thank you as she pulled a stool with her and plopped down by John’s bed. His breathing was even, deep and slow, probably from the medication that was keeping him under. She leaned against the bedrail, following the blue scales down his neck and out his shirtsleeve, down his arm to where it disappeared into the cuff of the restraint. His hands were still his, for the most part. Slender, like hers were. She’d put hers to use in her childhood playing the piano, he put his to use flying helicopters and puddlejumpers. Without conscious thought and because it seemed like the right thing to do, she slipped her hand under his. 

The scales were dry and, surprisingly, soft against her palm. She could barely feel his calluses, the ones he’d built up from shooting, or maybe where his hands cradled the controls of an aircraft. Still they were there, classic John Sheppard beneath the mutation. He was still in there, just like she knew he was. 

_Hang on, John,_ she thought with a slight squeeze to his fingers, _we’ll get you out of this. Just hang on._

* * *

Her first thought at Beckett’s new plan was that it was absolutely ridiculous. Upon further consideration, she changed her mind to believe not only did it _have_ to work, but that it _would_ work.

She spent an agonizing hour biting her fingernails and trying not to snap at anyone that got too close, parked on the steps in the Gateroom and not budging for anything, even a coveted Snickers bar. So they left her alone with her thoughts; thoughts about what would happen if – when – the plan worked, and how long it would take John to get back to normal. She thought about how the tension in her chest would finally relieve itself if – when – it worked, that she would have still have John and could have some semblance of normal back. Well, as normal as her life had become, anyway. 

But what she couldn’t keep out where the other thoughts, the dark ones that told her John wouldn’t survive. That he’d become a bug completely, or something much worse. That she’d lose the only family she had left in her life and become an orphan, an abandoned and unloved teenager in Atlantis. Or maybe they’d just throw her in a boat, give her some rations and say “See ya later.” Elizabeth wouldn’t do that, would she?

_You haven’t been very nice to people since you found out most of what was going on, especially Elizabeth,_ her mind pointed out painfully. She looked up in the direction of the woman’s office. Elizabeth had been just as scared for John as she was but did that give her the right to be rude to the woman? No, it didn’t. And that was the difference in both age and experience. Elizabeth could, for the most part, hide her emotions from others. She was a diplomat, she had to. Ali wore her heart on her sleeve for all the world to see. And now it was biting her in the rear.

And then there was the little fact that she was sure she’d sworn at both Elizabeth _and_ Carson, which was probably not the smartest thing to do. But she’d been so frustrated. She’d been so confused that no one would tell her anything – not what was going on with John, or what had caused it. And still there were holes in her knowledge, ones that she planned on rectifying with John when he was better, but holes were still holes. They were hiding something from her, something big and important and she itched to know what it was. 

The Stargate started to spin.

Ali pushed herself to her feet and retreated up the stairs to stand by Chuck. It was one of John’s rules for her while in the Gateroom, in case anything happened to go wrong and something unfriendly came through the Stargate. It was meant to keep her safe. Mostly it annoyed her. 

Lorne was first through the puddle, followed closely by the rest of the assembled team. Ali did a quick head count, frowning until she saw Ronon, John’s still body slung over his shoulder. Her heart and stomach did multiple loops. But Carson hadn’t called for a gurney or a medical team or anything, so that was reassuring. Unnerving all the same, but reassuring. 

She followed Ronon and Carson at a distance, wanting to give them space and knowing full well that Elizabeth was behind her. She waited politely outside the curtained area while Carson got John settled and hooked him up to an IV, administering what had to be the cure for this whole spectacle and gnawed on her fingernails some more. Elizabeth went right in, looking literally over Carson’s shoulder and Ronon took a seat in the waiting room, dwarfing a chair. Ali turned away from John to look at Ronon. He was as much a mystery to her as everything else in Atlantis was. She didn’t like that, either. 

“Little Sheppard,” he said and she nearly bit her thumb bloody. 

Ali went over and sat in the chair next to him. Instead of feeling intimidated by the sheer size of him, she felt safe. There was a reason this man was on her father’s team, and it wasn’t because of his hair, though it was really, really cool. 

“He’s gonna be fine.” 

She picked up an ancient copy of _Good Housekeeping_ , not surprised at all that Carson would have copies of those floating around the infirmary, and started to flip through it. “Yeah. That’s what it looks like.”

“He’s tough.”

She’d heard that before, too. “Yup.” Ali tried hard to relax, really she did, but she simply couldn’t get her body to cooperate. Her mind was still working over all the details she had and didn’t have, trying to make sense of it all.

“You’re frustrated.”

She started, shocked he’d pegged her so easily. “You could say that.”

“Why?”

Ali looked at her ragged fingernails. Her stress level had been through the roof lately and really, what was there to not be frustrated about at the moment? “There’s something they’re not telling me. Something I feel like everyone else knows but I’m missing. And part of it has to do with what happened to John, what he was turning into.” She drew her legs up onto the chair with her, curling as much as possible around herself. The soft denim against her cheek did little to soothe her. “There’s something I’m missing and it’s really frustrating.” She looked over at the area where John was, partially curtained off. “And I know he won’t tell me.”

Ronon knew immediately that no one had told her about the Wraith. As much as he knew she could handle it, as much as he wanted to tell her to make it easier for her, he knew it wasn’t his place. This was a decision that John had to make, that her father had to make. So, he settled for, “Wish I knew.”

She looked at him hard but couldn’t tell if he was lying to her or not, trying to make her feel better that she didn’t really have a clue about the biggest danger in the galaxy she was in. She gave a non-committal half shrug and looked over at John again. Neither Carson or Elizabeth were around and he seemed peaceful enough…maybe she could sneak over for a bit, just sit by him. She’d wished she’d had the forethought to go back to her room and grab a book or something, but she’d been so wound earlier. The first step was to uncurl her legs from the chair. 

Ronon “helped” her make a decision by giving her a firm but gentle shove out of the chair and in John’s direction. Ali shot a short-lived glare over her shoulder as she continued toward the bed, trying to be quiet.

John was on his back, wrists in the same padded restraints as earlier, blue scales glinting in the low light. She didn’t hesitate this time; she slipped her hand immediately under his and gave his fingers a slight squeeze. 

“He’s goin’ ta be alright, lass.”

Ali jumped, tightening her grip on John’s hand as she looked over her shoulder to see Carson, hands in his lab coat pockets simply watching. “Yeah,” she said, voice a little shaky. “Thank you.” She swallowed down phrases like _Thank you for giving hope back to me_ and _Why didn’t you tell me what was going on when this all started?_ “I’m sorry.”

Carson came to stand beside her. “Sorry fer what?”

She felt the blush creep up her neck. “Well…I haven’t exactly been the nicest person to you or Elizabeth lately. And that’s not fair; you were trying to do your job and I wasn’t exactly helping. So, I’m sorry for that. And I’m sorry that I swore.” Her mother had raised her to keep her language clean under penalty of washing her mouth out with soap well into her teenage years. She quite imagined that John would be the same way, which prompted the thought of whether or not Pegasus soap tasted better than Earth soap. Which made her want to giggle in a slightly hysterical way. 

“Everyone’s been under stress lately, Alison,” Carson said. “It got a little scary fer all of us. I can’t imagine what must have been goin’ through yer head, thinkin’ maybe yer goin’ ta lose another parent.” 

Ali looked over at him, shock on her features followed swiftly by gratitude that somebody understood. Somebody had realized what had partially been running through her head. Her lower lip wobbled. 

“I’m quite sure John’s proud of ye fer how ye did, holdin’ up against all that.” His voice was soft, sincerity in his blue eyes.

Ali sucked in her breath and released John’s hand so she could launch herself at Carson, soaking his collar with all the frustration, fear, and pain she’d felt since the entire thing started. It felt so good to let it all go.

* * *

“Hi, John.”

John cracked an eye open from his supposed “nap” and looked at his daughter, eyeing the book in her hand. This was his fourth day in the infirmary since Carson had stopped the conversion, aiding him in the process of, for lack of a better phrase, shedding his scales. There was still quite a bit on his neck and arm, especially on his right, but his eyes were hazel again and he kept waking up to more and more blue on the white infirmary sheets every day. And Ali kept him company, too, so he didn’t suffer too much boredom. She stopped by every morning, afternoon, and evening, either to read to him, talk about the goings on the rest of Atlantis as best she knew, or simply to keep him company. She’d been bringing books to read, too, and it was a good way to get him to relax. 

“Whatcha got, now?”

She held up the large, hard-cover book and smiled. She had a secret love of Jules Verne that he hadn’t known about until he’d been read _Around the World in Eighty Days_ in all its original glory. John had become quite the fan of Phileas Fogg since then, and was enjoying _Journey to the Center of the Earth_ just as much. 

“Where’d we leave off again?” she asked, sinking into the hard plastic chair by the bed and cracking open the thick volume. 

“Uh, he lost the stream,” John said. It was beginning to seem as though Harry got into more trouble than he did, which was something that made him grin. 

“Right,” Ali said, getting as comfortable as she could. She flipped through the pages, looking for the correct one and wondering why she hadn’t just used the stupid ribbon bookmark attached to the spine. “Don’t itch.” 

John wondered how she’d even seen him scratching idly at his forearm when he swore she was engrossed in searching for the right spot to start.

“Found it,” she said. She cleared her throat. “Ready?”

“When you are.”

She smiled. “ ‘No words in the any human language can depict my utter despair. I was literally buried alive; with no other expectation before me but to die in all the slow horrible torture of hunger and thirst’ don’t itch!”

John threw his arms up in exasperation and then sat on his hands. Uncomfortable and itchy, he settled back and listened to the sound of her voice as it waxed poetic over Jules Verne’s prose, thinking this was a much better way to spend time in the infirmary than cursing orange Jell-O and counting ceiling tiles. When he glanced over at Ali’s face – the excitement in her eyes, the happiness at sharing something that was so personal to her with him – there really was no better way.


	5. Integration: Innocence

**Summary for the Chapter:**

> Pegasus rarely plays fair. Life predictably goes to hell on Ali's first trip off-world.

Ali needed to talk to Elizabeth – more specifically apologize to Elizabeth – or she was going to implode. Or explode. Either one. And it would be extremely messy for someone to clean up later, and Atlantis had had a bit of time regrouping from the latest fiasco only a few weeks ago: John Sheppard attempting to turn into a bug. Ali shuddered at the memory.

_What I really need is a vacation,_ she thought. Here she was in a place most would consider the best place to get away from the world and she wanted out for a little while. Locking herself in her room for hours didn’t count, either. Head full, completely unsure what to do to even pass the time anymore, Ali wandered from her room through the halls of Atlantis. 

“You look lost, Little Sheppard.”

Ali stopped, not startled enough to jump. Calmly, she turned to face Ronon. “I’m not lost.” To emphasis the point, she passed her hand over the nearest door panel. It opened to a room with rows and rows of plants. _Botany. Awesome._ Her mind finally kicked into gear. “I came to see Parrish.” Her look dared Ronon to say otherwise.

Ronon decided that such a look was definitely a Sheppard thing because her father did that on occasion. Mostly on missions. 

Ignoring the six-foot mountain man behind her as much as possible, she started down a row of violet-leafed flowers. “David?”

Parrish’s head popped up from another row. He looked curiously between her and Ronon and then smiled, waving his good hand. The other was still encased in plaster, only with a little more graffiti than when she’d previously seen him in the cafeteria. 

“Hey, Alison.” 

She made small talk with Parrish if for nothing else than to pass the time, genuinely see how he was doing, and procrastinate in apologizing to Elizabeth. Ronon hanging over her shoulder didn’t help her nerves the least.

* * 

“I think Ali’s bored.”

Teyla paused, her forehead touching her knees and simply breathed. “How so?”

“She spends a lot of time in her room or on the balcony,” John said. “She just watches the ocean or watches people in the mess. I really think she’s bored.” _Or sad._ He didn’t say it; as far as he had come in terms of dealing with and expressing emotion, especially with Ali, he still had a way to go. They weren’t at the stage yet where they could both openly discuss feelings. John wondered then if they ever would.

“Is she having problems dealing with you nearly mutating completely into a bug?”

That had actually been his first inclination but every time he tried to bring it up she insisted she was fine and stared at him until he changed the subject. He’d wisely let it go, for the time being.

Teyla took his pensive silence into consideration and then said, “There are a number of safe, cautious worlds that you could show her. The Marniy people we visited last month have not had a Wraith attack in many months.”

John looked at her as though she had a squid for a head. 

She released her stretch and stood gracefully. “The Stargate is a natural wonder of this galaxy. The Marniy are good people, and Cale will be glad to see us again.” Cale, leader of the Marniy people, had assured them that any time the Lanteans wanted to stop by they were more than welcome. 

And Cale had a daughter that was around Ali’s age. 

John rolled the idea around in his head. It would give them both a little vacation, and Cale had assured them the last time that there hadn’t been a culling in years, barely any sign of the Wraith at all. Of course people wandered into the woods and failed to come out again, but that happened in every culture, didn’t it? Things happened. He’d seen enough to know that was a proven fact.

“I’ll talk to Elizabeth,” he conceded. 

Teyla nodded with a smile. Some time off for both John and Ali would be just what they needed.

* * *

Ali shifted nervously from foot to food outside Elizabeth’s office and, insides churning, finally plucked up the courage and knocked on the door.

“Hello Alison.”

“Doctor Weir.” She sat in the chair in front of Elizabeth’s desk. She decided this was one of those things that was best done quickly, like pulling a band-aid. “I just want to say I’m sorry. I was entirely unhelpful a couple weeks ago when John was having…issues…and I was wrong to take it out on you.” She relaxed her white-knuckled grip on the chair and told herself to breathe. 

“We were all under stress, Ali,” Elizabeth said. “Apology accepted but you were perfectly right. We were all stressed and scared. If you hadn’t been, I’d have thought you weren’t normal.”

Ali heard the unspoken _Or you didn’t care_ as clearly as if Elizabeth had said it. She ignored that. She did care about John. He was what she had.

“Because of this, on suggestion from John, I’m allowing you two a little vacation.”

Ali abruptly released the chair, completely unprepared for that. “A vacation?” Coming from a world that would consider Atlantis prime vacation property, she wondered what exactly Elizabeth was talking about. 

Elizabeth smirked. “Talk to John.” 

She looked quizzically at Elizabeth and realized she wasn’t going to get any more information. “Thanks.” She forced stiff fingers to detach from the chair and stood. 

“Ali.”

Ali was almost to the door when Elizabeth called her. She looked over her shoulder.

“If you need someone to talk to, I’m always here,” Elizabeth said, meeting Ali’s eyes. “About anything.” _Including but not limited to your father mutating into something strange._

She swallowed and nodded. “Thanks.” Ali left before she could embarrass herself further, heading directly for John’s hole-in-the-wall office. She hoped John wouldn’t beat around the bush at all, she really wasn’t in the mood.

* * 

Ali couldn’t believe it.

She stood in front of the active wormhole and simply stared at the blue expanse before her. It was breathtaking. So much, in fact, that she had to remind her lungs to keep inflating and deflating. 

_Wish you could see this mom,_ she thought. She looked over her shoulder for John, hooking her fingers in the pockets of the tactical vest she wore. It was a little big on her, as were the dark uniform pants and jacket, but John had said it was a necessity. He’d packed the vest especially for her, stuffing it with things that, if anything went wrong, she’d need. The trusty-as-ever Swiss Army knife was in the right bottom pocket. He’d made sure she knew where that was. 

“Cool, isn’t it?” John asked her softly as he stepped up beside her. Curiously, the only gun he wore was one on his thigh. That wasn’t to say he was unarmed; John was a soldier, through and through, and he would always be armed in one way or another. That much she knew, just from the way his eyes would harden when he was stressed or under pressure, the way he used the calmness in him to solve a problem in a time crunch. She wondered how he hadn’t shot McKay since the man was the complete and total opposite. Rodney was loud and complaining, venting his frustrations to the world when he was stressed. Then again, she marveled at the energy the man seemed to always have. Must have been the coffee.

“Very cool.” She smiled and looked at the puddle. The thing she had to walk through. Walk through a stable wormhole onto another world. 

No wonder her palms were sweaty. 

“Ready?” John asked, looking at the Stargate like it was something he did every day. 

_Well, duh, you moron, he_ does _do this every day._ Ali shook herself minutely and looked at John. “Ready.” 

She missed the pride in John’s eyes as she walked forward and disappeared into the blue. 

When Ali opened her eyes on the other side she was forcibly reminded of the semi-ruined vacation when she was nine. Her mother had insisted they go camping in some protected forest. The path and all the trees in front of her reminded her of the way she and Nancy had gone to the campsites; a good three miles from the parking lot. _That_ had definitely not been on the brochure. 

John was only a step behind her, clapping her on the shoulder as he moved toward the path. The wormhole disengaged and Ali stood rooted to the same spot, still marveling that she was _on a different world!_

“What was it like your first time?” she asked, jogging a little to catch up with John for fear of being left temporarily behind.

The elder Sheppard stuck in his hands in his pockets and smiled wryly. “I didn’t even know the Stargate or anything like it even existed until Antarctica.” Antarctica. The days when he’d simply been a rotor pilot in the Air Force, sent there by his commanding officers after what happened in Afghanistan. He remembered his first encounter with alien technology; piloting the helicopter with General O’Neill as his passenger and nearly getting taken out by an Ancient drone barely controlled by a skittish Scottish doctor who was more apt at repairing damage than causing it. 

“Yeah?”

John looked at the path. “Sat in a chair and it leaned back and literally there was a map of the universe above me. That’s when I discovered I have the gene.” He remembered the next part, too. Placed under Sumner’s command and literally on a one-way trip into the unknown. “My first trip through the ‘Gate was to Atlantis.”

She stuck her hands in her pockets, unconsciously mirroring him. “You guys didn’t know if you would be coming back, did you?” Ali worked hard to keep the bitterness from her voice. It wasn’t her fault that John hadn’t known about her, hadn’t known he’d had a reason to stay on Earth in the first place. She couldn’t blame him for something he didn’t know. If she couldn’t, then why did part of her want to?

He shook his head, knowing what she was thinking; if it had been a one-way trip, then why abandon her? That he hadn’t know he had a daughter seemed a weak defense. “Right. But things got better. They got tough, but they got better.” John chose to skip over the fact that he’d woken the worst threat in the galaxy and killed his commanding officer all in the same day. That would require an explanation of the Wraith and he wasn’t about to inform Ali of the danger. 

“Things always get better,” she murmured, more to herself than anything else. When she looked up again she froze. They were on the fringes of the village, well within the woods and away from the Stargate and the people – she was thinking seventeenth century Europe – were only giving them a passing glance or two to John but almost openly staring at her. 

Her cheeks turned pink. 

John gave her a gentle push toward the village where a man stood with a girl about her age, right behind her. Cale was a tall man, not as tall as Ronon, but tall enough to have a few inches on John. He had long blonde hair tied at the nape of his neck and the girl by him shared the same blue eyes and blonde hair. John gave Cale a smile as the girls sized each other up. 

John put his hand on Ali’s shoulder, amused at the complete turn around from curious and questioning to shy and quiet. Cale gave his daughter a nudge toward the Sheppards; John squeezed Ali’s shoulder.

“Hi.” Ali took a step forward automatically and gave the other girl a wobbly smile. She almost turned around and asked John what the hell he was thinking, that they were supposed to be on vacation or something, but she didn’t. She didn’t want to look clingy to the other girl who was looking at her in much the same way.

“Want to see the ruins?”

Ali looked over her shoulder at her father who nodded, and then moved forward to the other girl. “Okay.”

“Keep your earpiece in,” John reminded her, watching the two walk away, conversing halting until they both laughed at something. John watched her until they disappeared into the fringes of the forest. 

“So, that is your daughter?”

John shoved his hands back in his pockets and started toward Cale’s home. “That’s my daughter.”

“I thought you had no children.”

He winced. Long conversations with Cale had had John explaining that he and his wife were no longer together and that he had no children. Ali had just defied that, rendering him a liar to Cale. “I didn’t know I had a child.” _Much less a teenager._ “My wife didn’t tell him.” He felt a stab of guilt of blaming a dead woman. 

“And your wife is with you too, now, yes?” Cale had his hands folded behind his back, a thoughtful pose. 

John looked at the dirt beneath his feet. “Uh…she died recently. That’s why Ali is with me.” _Stuck in Pegasus whether or not she wanted to._ “Atlantis is becoming home now.”

Cale smiled. “She’ll get used to it. She’ll get used to you.”

John had no desire to mention that she’d been witness to his slow slide into madness while turning into a bug. The implication of that, the “what if’s” were probably still terrifying her, the possibility of losing her only remaining parent. John himself was still coming to terms with what had happened to his body and mind. He still shivered when he remembered the way he’d felt, how scales had felt better and safer than fragile human skin. The way his eyes had changed to process light differently, more deftly than weak human eyes. And John remembered the way, especially in the cave, that his mind had called to others of his kind. It still freaked him out. And he had no desire to share that with Ali’s already ragged nerves. That’s why he’d agreed and argued for her to have this little vacation of sorts. She needed to stay sane. Hell, he needed it just as badly. 

“Deep thoughts, Sheppard,” Cale said. “Don’t worry, Maril will take good care of Ali.”

“I’m not worried about that.” He scrubbed a hand over his face. “Things have been….difficult, lately.” He missed the shadow cross Cale’s face. 

“There have been no threats of the Wraith, correct?”

John looked sharply at Cale and noticed the man seemed uneasy. He stopped short with the sudden fear that something was wrong. “Cale?”

The other man looked at John briefly before looking away.

“How long?” John asked, fingers tightening compulsively on the space where his P-90 should have been. 

“There hasn’t been a major issue,” Cale said, continuing his walk. “People go into the forest and they either don’t come out or…we find them. It seems to be only one.”

One Wraith was still a Wraith. Still dangerous. 

John wasn’t even on a mission and it was going pear-shaped.

“Those who have encountered it have gone deep into the forest,” Cale said, hoping to placate his friend and make retributions for the slip-up. He looked John in the eye and said, “I wouldn’t let my own daughter wander the forest to the ruins if it wasn’t safe. And I would not have allowed your daughter to go, as well.”

John couldn’t doubt the sincerity in those blue eyes. Still, he reached up and tapped his radio. “Ali?”

There was no response. 

He refused to let his heartbeat kick up. She probably hadn’t heard him. He tried again. “Alison?”

A scream filled the radio and echoed through the woods.

* * *

Ali had loosened up by the time she and Maril reached the ruins. Her first impression was that it was eerily similar to Stonehenge, only, a little better constructed and with a solid ring of rock around the top of those that stood vertical. There were sets of stairs leading to the top and surrounding the entire thing was the remains of a wall. Upon further consideration, Ali thought it was an appropriate mix of _The Lord of the Rings_ and Stonehenge. It was quite fascinating.

“These are the ruins,” Maril said, pushing her long blonde hair over her shoulder. “They were here long before our people came to this world, when we left the Homeland to escape the Wraith.” She motioned to the groups of smaller children playing among the vertical stones; a game of hide and seek or something similar. “Many of the children play here.” She motioned for Ali to follow, climbing up a set of crumbling stairs to the top of the ruins. 

They were about ten feet off the ground. Ali turned slowly in circles, taking in the expanse of the trees and the children on the ground below her. A flash of white to her right caught her attention and she turned, trying to peer through the underbrush and tree branches. There was something out there, something sneaking around. A quick look at the children confirmed that none were wearing white – it would be too easily stained and dirtied. Impractical for children. 

The white flashed again and Ali knew it was no child. It was taller, taller than John and most definitely _not_ native. 

“Maril,” Ali said, reaching to tap the other girl on the arm without taking her eyes from where the thing was. “What’s that white thing in the trees?”

“White thing?” Maril looked in the same direction that Ali was and her heart nearly stopped. It was impossible…they’d escaped them, years before. “Wraith,” she whispered, more of an exhale than a conscious decision to speak. Without another word she raced back down the crumbling steps, rounding up the children as quickly as she could, speaking hurriedly and keeping her voice down.

Ali stood on the ruins, still staring at the forest. It was getting closer, whatever the thing was, she could see its long white hair, glinting in the light that filtered through the leaves. It paused between two pines and locked eyes with her. Ali didn’t have to know what it was to know that it was dangerous and deadly. She recoiled as it smiled, moving forward deliberately now, stalking toward her. Heart thudding in her chest she froze. 

“Ali! Ali get down here!” Maril yelled, herding the children down toward the path where they could run back to the village. “Ali!”

It was the fear in Maril’s voice that got her legs moving. Shaky steps took her to the stairs and she more stumbled down them that actually walked, landing hard on the rough ground and immediately looking for whatever the hell was stalking her. Her radio crackled, startling her further but she couldn’t move. She didn’t understand why it was so fixated with her. The radio crackled again and she hit the button.

A child looked back from the path and screamed, pushing at its fellows to get through. Soon all were sprinting down the path. Maril grabbed Ali by the arm and dragged her away from ruins and into the woods, away from the path and the children, hoping to lure the Wraith away from the village. It was ingrained responsibility as Cale’s daughter; protect the others, especially the children. 

Ali’s fingers fumbled for the radio, dislodging it and dropping it to the ground. She followed Maril into the trees, flinching openly when the Wraith reached the ruins behind them and screamed, “Lantean!” She didn’t look back. Especially when she knew they were clearing a path a blind man could follow easily.

* * *

Cale and John were nearly run over by the group of screaming and crying children on the path to the ruins. Cale caught the lead boy easily, swinging him up into his arms and whispering soothing things while looking for his daughter. John looked at every face and up the path, hoping that Ali would be coming around the corner at a dead sprint.

“Back to the village, quickly,” Cale ordered, putting the child back on his feet. He waited until they were all running along again before continuing toward the ruins, already knowing what they were going to find. 

The ruins were empty.

John looked around, trying to quell the screaming panic sitting below his breastbone. There was a Wraith in the area, his daughter was missing, and he had royally screwed up. Come to think of it, he’d royally screwed up everything in her life. He hadn’t known she had existed and therefore wasn’t there while she was growing up. On top of that was that she’d left Earth on a one-way ticket to Pegasus to stay with the father she’d never met, much less probably even liked. And now she was going to be fed on by a Wraith if he didn’t find her. John couldn’t even begin to understand how things had gotten so screwed up. 

One thing was simple. He _had_ to find her. If not for her sake than for his own because he wasn’t sure he could handle losing her.

* * *

Ali leaned against a tree, trying to catch her breath, and was insanely glad she had run track for so long. Hurtling had been a little out of her realm then but now she figured after hurtling so many broken branches and stumps she might have done really well. Hell, she might have been able to do the steeple chase at this rate, too. The thought almost made her laugh. She would have, too, if she hadn’t seen the anger on Maril’s face.

“What were you doing back there? Do you have a death wish or something?” Maril demanded.

“What?” Ali stood straight and stared at the other girl, confused. “Death wish?”

“That was a Wraith!” she exploded, throwing her hands up in the air. “When you see a Wraith you run! Don’t you know that?”

Ali felt as though she was missing a very important concept because she wasn’t feeling the same fear that Maril was. “Wraith? What’s a Wraith?”

Maril froze, disbelief on her face. “You don’t know what a Wraith is?” She was quieter now, almost in shock. If this girl in front of her was John Sheppard’s daughter she honestly wondered how she had survived as long in Pegasus as she had if she didn’t know what the Wraith was. How could she not know what John had awoken? The threat they all faced?

“No.” Ali leaned against the tree again. “What’s a Wraith?”

“A Wraith is the most dangerous thing,” Maril said, feeling surreal that she was explaining what every child knew from infancy. “They suck the very life from you, with their hand. All that sometimes remains is the dried, dead husk of a person you used to know.” She wrapped her arms around her middle. “You used to love.”

She pushed away from the tree, horrified. “They suck the life from you?” She thought immediately of vampires and the notion was ridiculous. Except that she’d seen a Wraith and the deadliness of it was something that was stuck with her. She paled, her knees giving out at the thought that _everyone_ in the Pegasus Galaxy must have known about the threat. They had to, in order to survive. 

But she hadn’t. John hadn’t –

John. John had let her wander off on another world – a world that had a Wraith on it – and hadn’t warned her about it. She couldn’t help the thought that crossed her mind – did John hate enough to want to make sure she never came back? Was this some sort of test or was this a way to get rid of her permanently? She thought things were getting better between them, they were finally connecting. It was a slow process but it was better. They were getting along, trusting each other. 

This was way worse than watching him turn into a bug. 

Ali looked up at Maril and from the look she was getting knew she looked as broken as she was feeling. Broken and betrayed. 

“I’m sorry,” Maril whispered. 

“Not your fault,” Ali said, getting back to her feet. “You have a father who loves you. I have an Air Force pilot without a conscience.” They were harsh words and she might regret them later but she didn’t care at the moment. All she wanted to do was survive long enough to get off the planet, get back to Atlantis and never leave her room again. That sounded like a damn fine plan. 

“Okay,” she breathed. “What do we do now?”

Maril shrugged. “We keep moving so he doesn’t find us and hope that my father and yours can track us.” She didn’t miss the flinch that ran through Ali at the mention of John as her father.

“Then let’s go.”

* * *

It was a sheer accident that they found the ravine. They would have gone right past it if Ali hadn’t had the luck to walk too close to the edge and the ground gave way beneath her feet. Maril screamed, backing away so as not to follow her new friend to the bottom. Thankfully it wasn’t a far fall; Ali landed hard in the mud and rolled, ending up on her back in the stream at the bottom. The sky above her grayed for a moment as she reminded herself to breathe.

“Ali?” 

“M’fine!” She called back when she could, rolling onto her side and wincing as she realized her entire backside was soaked. _This just gets better and better._ She watched Maril slip and slide down the ravine wall to join her, helping her to her feet. “I’m fine.” She refused to think that she reminded herself of John during the whole bug incident. 

Maril nodded, taking Ali’s statement at face value. “This stream runs by the village. We can follow it back, and hopefully my father will catch up with us.” 

“Fine,” Ali said, wrapping her arms around her middle. “I just want to go home.” And she wasn’t talking about Atlantis. 

Maril wrapped an arm around Ali’s shoulders and squeezed. Ali leaned on the other girl briefly and the two started walking. They hadn’t been walking more than fifteen minutes when they heard voices ahead. Maril stiffened and approached cautiously, relaxing visibly when she recognized fellow villagers. 

“Maril!” A gangly boy waved emphatically at her, his companion leaning on the shovel he held. 

“Aerik, Illen,” Maril said, leaving Ali to give the boys a hug. She instantly felt safer. “This is Ali, a visitor from Atlantis.”

Ali cradled her left arm, the throbbing one, near her body and gave the boys a smile. “Hi.” 

Maril gave her an assessing look and when she turned back to Aerik her eyes widened. She stumbled back, mouth open wordlessly as the Wraith landed in the ravine and snapped Illen’s neck like it was nothing. Aerik pushed Maril toward Ali and placed himself between the Wraith and the girls. Maril positioned herself in front of Ali and held her head up. She could might possibly die but she was going to do everything she could to save her new friend. 

“I want the Lantean,” the Wraith snarled, exposing his sharpened teeth. 

Ali’s knees shook, fear coursing through her. The Wraith wanted her? Just her? It must have been the uniform. 

“You can’t have her,” Aerik said. His voice shook less than Ali had figured it would. She was two people away from the Wraith and was still terrified. She admired his courage to stand up to it. 

The Wraith shot its hand out, latching onto Aerik’s chest. The only one who didn’t scream was the Wraith as he sucked the life from Aerik’s body, grinning malevolently. 

Ali had the fleeting thought that she was going to die. It was slightly confirmed as the husk of Aerik’s body dropped to the ground. She wasn’t going to be able to sleep for weeks, the nightmares would be so bad. Chalk up another reason to stay forever in her room. Between this and the bug, she was going to be scarred for life. 

The Wraith stalked toward them. Ali bit her lip and shoved Maril to the side, toward the stream and stared at the approaching Wraith. 

“What do you want?” She was impressed; her voice didn’t crack or shake.

“The address to Atlantis,” it growled. 

Ali almost cried in relief. It wanted something she honestly couldn’t give because she had no idea what he was talking about. “I don’t know what you’re talking about, really I don’t.”

It closed the distance between them and backhanded her across the face. Ali landed on the ground again, blood dripping slowly from her nose and realizing she was going to have a spectacular black eye. 

“I don’t know what you’re talking about, really I don’t,” she repeated, tears forming in her eyes. Is this what John wanted? For her to be killed by a Wraith over information she couldn’t give? 

The Wraith reached toward her, it’s hand stretched toward her and she closed her eyes. It would be quick, sort of. And painless. Maybe. Ali was afraid to die at such a young age, but the good thought she had was that she’d join her mother. She’d be back where she wanted. With someone who loved her. 

Gunshots filled the air and the Wraith jerked forward, almost falling onto her. It fell to the ground beside her, blood dribbling from the holes in its back. Ali looked up to see John and Cale, the gun still pointed at the Wraith beside her. 

_I was bait,_ her mind whispered harshly. She recoiled into herself and tried as hard as she could to keep the tears from coming. She failed. When John reached to help her up she flinched away from him, distrust in her eyes. She allowed Maril to assist her and kept a healthy two feet of space between her and John. 

John didn’t understand why Ali was looking at him like that, why she wouldn’t allow him to touch her. He gave her the space she wanted on the way back to the village, smiling when she gave Maril a hug and appropriately confused when she wouldn’t even look at him on the way back to the Stargate. 

“Are you okay?” John hadn’t been able to get close enough to really see if she was all right. The bloody nose and forming black eye were obvious enough, and he suspected that she had hurt her arm from the way it was held close to her body. 

“Fine.” The answer was short and curt, nothing like the Ali he had started know. 

John dialed the ‘Gate and went to put his arm around her. She ducked under the attempt and walked away from him. His breath left him as though she’d punched him in the gut. He rubbed his forehead, noticing she was covered in mud from head to toe in the back. He tried once again in the Gateroom to put his arm around her and she did the same routine, accompanied with a hissed, “Don’t touch me.”

Ali ignored all the stares and whispers and practically ran for the infirmary. Her head was pounding in time with her arm and she wanted nothing more than to lie in bed and sleep for the rest of the day and then implement her plan to become a hermit. She wasn’t ever coming out. John had..she didn’t even know what John done, really, but it was hurtful and she was confused and alone than when she’d come to Atlantis. 

“Alison?”

Ali went through the infirmary and hopped onto a bed. “Doctor Beckett.” She ignored John as he came to stand at the foot of the bed. 

“That’s quite the bruise yer gettin’,” Carson said, quickly pulling on a pair of gloves and gently probing her cheekbone. He wiped the blood from her nose with a gauze pad, pleased when it wasn’t bleeding any more. “Ye got lucky yer nose didn’t break.” When he inspected her forearm he deduced it was broken – a clean break – and she fisted the sheet while he set it. John wanted nothing more than to hold her hand while Carson fixed her, but he didn’t dare move, knowing she’d reject him again. Carson applied a cast, gave her some pain medication, and then sent her on her way. From the looks of things, there was quite a big rift between the two Sheppards. And knowing John’s communication skills (or lack thereof) he silently wished them the best of luck. Ali had done wonders for John, made him the more personable and smiling since she’d been there. Carson knew that whatever had happened on that planet had caused that to go straight down the tubes. 

Ali headed for her room without a second look at John. 

“Alison!” 

She paused outside the transporter, unable to ignore the tone of his voice. Biting her lip, she turned and faced him. “John.”

“I’m sorry.” 

Tears came back to her eyes and her temper flared. “You’re sorry? You’re sorry? For what? For nearly turning into a bug? For nearly leaving me an orphan?” She shook her head. “Or are you sorry that you didn’t tell me what every kid in this damn galaxy knows? That there are space vampires out there, waiting to suck the very life from you?” Tears rolled freely down her cheeks. “Maril asked me if I had a death wish, because when that thing first appeared I just stood and stared at it. And it wanted to kill me.” She wiped at her face, wincing when she rubbed her cheek too hard. “But she had faith. She knew that her father was going to come for her. Save her. Because that’s what fathers do. And you…you I don’t know about. You keep secrets from me, put me in dangerous situations without me knowing and without knowing everything, and…” she looked him in the eye, trembling with anger. “I think I know my mother didn’t tell you. Why she didn’t let you know that you were a father. Well, I don’t have a father. I have an Air Force pilot who doesn’t give a damn.” She turned her back to him and stepped into the transporter. 

John leaned against the wall, feeling his legs turn to Jell-O and then slide out from under him. So there it was. _I have an Air Force pilot who doesn’t give a damn._

Where the hell did they go from there?


	6. Integration: Proceed with Caution

**Summary for the Chapter:**

> The Sheppards attempt to fix their communication issues.

_”I don’t know what you’re talking about, really I don’t,” she said and the Wraith advanced on her, backhanding her across the face. When she looked at him, blood dripping from her nose, he wasn’t a Wraith anymore. He morphed slowly into John, only not human John. It was the John that she’d watched devolve into madness, Bug John, and he moved toward her, his clawed hand still the feeding hand of a Wraith, the same one that had killed that boy on that planet. She was still as he reached for her, intent on draining the life from her, a strange chuckling from him growing into a maniacal laugh as he thrust his hand against her chest, over her heart…_

Ali sat upright, a scream struggling to escape her throat, her left hand fisting the sheet. She panted, hair sticking to her sweaty forehead and thought the lights on. She was blinded for a moment and took deep breaths, trying to get a handle on her breathing. The room slowly focused and she scrubbed a hand over her face and into her hair, pushing it back. 

It had been three days since her disastrous first trip to another world (if she didn’t count coming to the Pegasus Galaxy at all) and the only night she hadn’t had a nightmare had been the first night. That was only due to being on some pretty good pain medication, courtesy of Carson. Her broken arm didn’t hurt anymore, thankfully, and she’d dropped the remaining blister pack of pills in her desk drawer for when she would need them next and hadn’t given it another thought. 

And as much as she tried she couldn’t get the other stuff out of her head. Namely, the Wraith and John. 

She didn’t bother to look at the clock as she threw back the covers and got out of bed. When she’d lived on Earth and had a nightmare she had gone down to the back deck and simply looked at the stars, looking up at the infinite universe. Since she’d moved to Atlantis, the many balconies around the city had become her quiet places. When she’d gotten her own room, she’d moved a chair onto the balcony and sat out there for hours, simply listening to waves lapping against the city, lulled by the rhythm of the ocean. She grabbed a sweatshirt from the back of the desk chair and headed for the balcony.

The floor was cold on her bare feet, the constant breeze off the water making her glad she’d brought a sweatshirt. She leaned against the railing and looked out into the darkness, lights from various rooms in the city casting a glow on the gentle waves. It was quiet, for the most part, and when she looked at the sky, the infinite stars, it reminded her of home. It had been okay for a little while, being in Atlantis with John. She’d started to let it be her home, her new place. Almost a way to start over. 

Earth was home to her again. Atlantis felt foreign now, John a stranger once more. 

Ali knew she’d been harsh but this wasn’t easy for her. He wasn’t the one who’d been asked to give up everything he’d ever known and be transported to another galaxy to live with a complete stranger. Just because they shared the same hazel eyes and some DNA didn’t make them family. She still didn’t know the man everyone expected her to call her father. And John sure as hell didn’t know her. He’d lied to her. Maybe not outright but he hadn’t told her the entire truth. He’d kept something vitally important from her and, in reality, she could have died from it. 

_He was protecting you,_ the voice in the back of her head whispered. _Protecting you because he loves you._

“Yeah right,” she snorted to the night. If he loved her he would have told her, not let her flounder on her own the way he had. She took one last look at the dark waters and went back inside, absently braiding her hair. 

And had the sudden craving for a cup of tea. 

With nothing better to do and not feeling the least bit tired, she slipped on her sneakers and headed for the cafeteria. The hallways were empty; anybody in their right mind would be sleeping. The only people up were either Marines on duty or scientists, too absorbed in their work to notice the time. So, logically, the cafeteria was empty as well. Lo and behold, next to the coffee that was out all the time, was hot water and tea bags. Scientists could run on anything caffeinated, apparently. 

Ali felt instantly better when she’d seated herself at a table, steaming mug of tea in front of her. The emptiness was a sharp contrast to the rest of the day when it was a constant hub of motion and people. She looked at the various tables, remembering those who usually sat there; how the scientists would gather in the corners, talking excitedly (sometimes too excitedly) and how the Marines would eat together, especially those on ‘Gate teams. She skipped over the table that she had sat at with John and his team, looking instead into the depths of the mug. The memory came sudden and unbidden.

_She blamed her huge history test on her inability to sleep._

_When she was tired of sighing and staring at the ceiling, she rolled out of bed and headed downstairs to the kitchen, truthfully heading for the deck. What she hadn’t expected was her mother sitting in the kitchen, idly dipping a teabag in a steaming mug of water._

_“Mom?”_

_Nancy looked up and smiled at her daughter. “Hey baby. Can’t sleep?”_

_Ali shrugged. “Not really. Can’t shut my mind off.”_

_“That history test is really bugging you, isn’t it?” Nancy recalled the way Ali had been staring at her textbook for hours the previous nights, all in preparation for the test was going to determine if she would go on to AP History the following year, her junior year. It would be a big accomplishment for her; she loved her daughter but Ali was positively lousy at history._

_“Yeah,” she said, sinking into the chair across from her mother. “I just…I want to do well.”_

_“Your dad’s a math geek. Like you.”_

_Ali looked up, surprise in her eyes. “Really?”_

_Nancy smiled. “Really. I was never that good with numbers. I had to try really hard. And I remember what my father said to me, one time when I was studying for this math test. He said, ‘Do your best. It’s okay to fail if you’ve given it your all.’ Just give it your all, sweetie.”_

_She smiled and yawned. “Thanks, mom.”_

_“Get some sleep honey.”_

_Ali kissed her mother on the cheek and headed back toward the stairs, pausing by the mantle. The light from the kitchen was barely enough but it let her see the photo, the man in his dress blues. Her dad. Who was a math geek just like her._

Ali watched a tear drop from her nose into the mug. 

“Alison?”

It was spoken soft enough for her not to be startled. She wiped at her eyes with her sleeve and turned her head to see Carson, still in his white lab coat with a steaming cup of something in his hands. “Hi. Doc.”

“May I sit?”

She wiped her eyes again, hoping he wouldn’t ask if anything was wrong and nodded. He sat across from her. She noticed he had tea, too. 

“Workin’ late?” she asked with a hint of a smile. The silence was a little much for her; too easy to hear the ghosts in her head. 

“Aye.” His blue eyes were tired. “How’s yer pain level?” The ever-present doctor in him rose. She smiled a little wider.

“It’s good,” she said, holding up her cast for his inspection. “Doesn’t hurt.” She put it back in her lap and took a deep breath, hoping she didn’t look as broken as she felt. It was starting to be a habit, breaking in front of Carson. First in the infirmary and now, in their impromptu tea-date in the middle of the night. 

“Can’t sleep?”

Ali played with the tag on the end of the string attached to the tea bag, avoiding his eyes. “Sort of.” 

Carson knew nervous fidgeting when he saw it. “Is it about John?”

She let the tag drop, watching it bounce against the cup. “I don’t get him,” she said softly, more to herself than him. She looked up. “Why did he lie to me? Why didn’t he tell me?” She paused. “Why didn’t you tell me?”

He took a sip of his tea. “It wasn’t my place ta tell ye.”

Ali drew her legs up and wrapped her arms around them, balancing on the small seat and feeling very vulnerable. “Because you aren’t my dad.”

“Exactly.” Carson gave her a small, reassuring smile. “He cares about ye, Ali. Really he does.”

She looked away, focusing on the tile on the floor instead of the kind-hearted Scot who was telling her something that was glaringly obvious. “He’s got a funny way of showing it.” She looked up at him again, letting him see the pain and betrayal in her eyes. 

“’Cause he loves ye.”

She couldn’t keep the derisive snort from escaping. “Like I said. He’s got a funny way of showing it.” 

Carson sighed tiredly, rubbing his eyes. He stood, preparing to leave. “He loves ye, Ali. Talk ta him and ye’ll see that.” From the stubborn set of her jaw, he knew that she had inherited more than John’s hazel eyes. He needed some sleep if he was going to have a hope of combating this. And he was going to need help.

* * *

John had come to the harsh reality that his daughter was ignoring him.

It hadn’t been easy and it hadn’t been fun, but that was the reality of the situation. He sat with his team and looked across the cafeteria where she stood, tray balanced awkwardly between her good hand and the one with the cast, and wanted nothing more than to go over, take her tray from her, and have her sit with him for lunch like she used to. He also knew any attempt to do such a thing would cause her to either act like she hadn’t noticed him or flee the cafeteria all together. 

The knife twisted a little further in his gut. 

“Just go get her,” Ronon said. He’d been watching Sheppard stare longingly in the direction of his daughter since she’d walked in. 

“She doesn’t want to talk to me,” he said, stabbing his untouched potato with more force than necessary. “She doesn’t even want to see me.” He couldn’t keep the disappointment and hurt from his voice, despite his best efforts. 

Rodney leaned around John to look at Ali. She looked utterly lost and alone. “At least make her sit with us. She looks like an idiot.”

John poked him in the ribs hard enough to make his eyes water. “If she doesn’t want to sit here, she doesn’t have to.” The parent in him didn’t want to see his child suffer, even if it was finding someplace to sit in the crowded cafeteria. 

In the end it was David Parrish who saved them both; John from his indecision and Ali from looking like a complete idiot. He swooped up from her left, nudged her cast with his own, and escorted her to a table full of botanists. 

Both Sheppards let out identical sighs of relief. Ronon thought it was quite odd.

“She has to talk to you sometime,” Rodney said, stuffing his face once more. 

John snorted inelegantly. Ali was just as stubborn as he was, maybe more. If she never wanted to speak to him again, she would find a way to do it. Hell, he hadn’t seen her socially since she’d gotten her cast on in the infirmary. Even then she’d been doing her best to ignore him. So far it was working. 

“I’m right, though, aren’t I?” Rodney continued, oblivious to John’s inner turmoil and the fact that Ali hated her father. “You two have got to communicate at some point.”

“And when did you suddenly become a parent, Rodney?” John growled, glaring at McKay. He threw his fork on his tray, too frustrated to have much of an appetite anymore. “This isn’t easy. She won’t even _look_ at me.”

“Who is the adult in the situation?” Teyla asked, eyebrow raised skeptically. “She’s hurting, John. She’s alone and vulnerable. She needs her father.”

“Well according to her she doesn’t have a father.” He put his elbows on the table and dropped his head into his hands. “She has, and I quote, ‘An Air Force pilot who doesn’t give a damn.’”

Even Rodney had nothing to say to that. 

“John,” Teyla said, waiting until he picked his head up and looked at her. “You need to talk to her. I would be more than happy to act as a mediator. I am sure Kate would as well.”

John snorted. The last thing he needed was a shrink trying to help him manage his kid and his life. 

“Think about it, at least, John.” 

He tried very hard not to think about what had happened the last time he’d thought about a suggestion of hers. He knew she had to feel guilty over that; it had been her overall idea, really. Not that he’d bring it up. He had enough issues to deal with and trying to persuade Teyla that it wasn’t her fault that things had turned out the way they had was something he couldn’t handle at the moment. He was actually working very hard to keep a tenuous grip on everything. 

And whether he wanted to admit it or not he was sliding. 

John looked over his shoulder, scanning the cafeteria until he found her, still at the table with the botanists. Her face may have looked relaxed, there might have been a smile on her face, but from the stiff set of her shoulders she was anything but comfortable. 

_Well that makes two of us._

* * *

Ali made it three more days when she got a visit from Teyla.

The Athosian woman showed up outside her door, incense in one hand and the request to simply “hang out.” Ali gave her a look that was plainly mistrustful, thinking it was a ploy on her father’s behalf, and relaxed only slightly when Teyla said all she wanted to do was “talk.” Ali had a base idea of where the “talk” would be heading but decided to give her the benefit of the doubt, knowing if she really wanted her to, all she had to do was request Teyla to leave and the woman would go.

They sat on the balcony together, staring up at the stars for long, easily silent minutes. 

“Love comes in many forms.”

Ali was tempted to look at the nearest clock to see how many minutes it had been. She knew this was coming and said nothing, hoping Teyla would get the hint.

“John loves you.”

_At least she’s blunt,_ Ali thought. She drew her legs up, wrapping her arms around her knees. “Sure.” Though she said it she didn’t believe it. 

“Alison, please,” she said, sounding properly exasperated. “This…rift, between the two of you isn’t healthy.” 

“Yeah, well, he should have thought of that when he made the decision to lie to me,” she shot back, her temper rising. She was getting so tired of listening to people come to John’s defense. Who was defending her? Who was aware of the fact that he’d lied to her? That he’d hid something so vital from her? Who understood that? 

“He did not lie to you – ”

“He didn’t tell the truth, either!” She shot to her feet, turning away from Teyla and crossing her arms over her chest. Anger pulsed through her. Why couldn’t someone see her side? Why did they love and approve of John more than they did her? His life hadn’t drastically changed. He hadn’t been uprooted and given to a stranger. Tears prickled her eyes. 

“He wanted to - ”

“Wanted to what? Protect me?” Tears leaked down her eyes and she spun angrily to face the other woman. “Oh, and he did a great job of it, too! He almost got me killed! Fed on by a Wraith!” She laughed, the sound more than a little hysterical. “He could have taken a lot of time off the years I’d have to spend here. John probably would have approved.”

“Alison!”

Ali shook her head, crying openly now and filled with righteous anger. “You don’t get it, do you? You can’t see my side. You can’t see that he lied to me. You can only see your precious friend, your team leader. You can’t see the man that made a mistake.” She sank to the floor of the balcony, the railing rungs digging hard into her back. She looked up at Teyla. “He didn’t want me in my galaxy. What makes you think he wants me here?”

Teyla was silent for a moment. Then said softly, “Because he loves you.”

She wiped her nose on the back of her sleeve. “Tell it to someone who cares.” She stared at the ocean. “Just go. Please.”

Teyla didn’t want to, but left anyway, realizing she wasn’t going to get anything more out of Ali that night. Still, she’d come a long way to realizing what exactly was wrong. 

A few balconies down John gripped the railing hard. His own daughter really _did_ hate him. And there was probably nothing he could do about it.

* * *

John Sheppard was amazed to be alive at the end of the day.

It was one of those crazy things. His head had been completely elsewhere, focused on his current situation with Ali and how she’d been absent from the Gateroom when he’d left for a mission. He’d completely missed the sharp turn in the path and not even Ronon’s reflexes could grab him in time before he’d tumbled down the ravine, bouncing like a rag doll until coming to a stop at the bottom. It was a wonder he hadn’t broken his neck. He’d damn near broken his leg. As it was, he’d popped a shoulder out of socket, busted more than a couple ribs, and had whacked his head more times than was healthy. He wasn’t even conscious when he’d stopped rolling at the bottom, half his body in the small stream of water in the belly of the ravine. Ronon had run back to the Stargate to dial Atlantis while Rodney and Teyla slid carefully down the ravine to get to him; Rodney doing his usual amount of freaking out and, Teyla her usual calm self with just the right hint of worry. 

John had come to the first time in the jumper, immobilized against a backboard with Beckett attempting to shine a penlight in his eyes and being unable to move away from it. He’d blacked out again when they put his shoulder back into place and woke up again in the infirmary on Atlantis, his head one massive ache and the ever-present knife twisting in his gut that Ali wasn’t parked in the chair next to the bed like she had been when he’d been turning into a bug. A too-honest nurse had confirmed for him that she hadn’t stopped by. 

And didn’t that just suck like a Wraith. 

He must have drifted off because the next time he did wake he found he had a visitor. One look at Elizabeth’s face informed him that he should have kept sleeping and/or still been unconscious. 

“John,” she said in all seriousness, “we need to talk.”

His head started to pound at his temples. Did he have a concussion? That would really make sense if he did. 

“This is getting ridiculous,” she said and he knew he was in for an ass-reaming of monumental proportions. “I don’t think I need to remind you that you could have broken your neck during that fall. All because you weren’t watching where you were going. Rodney I could see doing this but, in all seriousness John, whatever is going on between you and your daughter needs to be fixed. Alison looks completely exhausted from what I’ve seen of her, like she hasn’t been sleeping. You don’t look much better and your focus has been terrible. You fell in a ravine, for God’s sake. Unless you’d like me to take you and your team off rotation, you _will_ fix whatever the hell is going on. And you _will_ do it soon. I can have Kate recommend daily sessions if the two of you need someone to mediate, but this absolutely cannot continue. So get your head out of your ass and communicate with your daughter.”

John tried to sink through the bed and the floor, hoping to escape the fire in her eyes. He was not successful. His head continued to pound. He’d almost rather be back in the ravine.

* * *

Ali heard vaguely through the grapevine about John’s release from the infirmary a few days after it happened and tamped down on her worry. She felt guilty that she hadn’t gone to see him while he’d been that, that it looked like she didn’t care, but everyone assumed she still loved him right? Everyone assumed that for him.

When she returned from breakfast she saw a note attached to her door from Ronon, telling her he was in the gym if she’d like to have an early lesson. With nothing better to do, she traipsed down to the gym, wondering if he was going to make her wield a stick or something with her left hand, make her able to defend herself just as easily with her weak hand as with her strong hand. What she didn’t expect was to see John standing in the gym, hands in his pockets and looking like he’d seen more than a few miles of bad road. Her face heated, another feeling of betrayal coursing through her and she turned immediately on her heel with a muttered curse. But no matter how much she tried it, the door wouldn’t open. 

John was still Atlantis’s favorite.

“Alison.”

She closed her eyes and inhaled through her nose. “Let me out.”

“No.”

Ali spun again and gave him a look that would have curdled milk. 

_Definitely my kid,_ he thought sagely, his headache a mild irritation at his temples. 

“Let. Me. Out.”

“Not until we talk about this.” John had spent the past few days reasoning with himself that he had let this go on too long. It had taken him the threat of being grounded to finally realize something was wrong that needed actual fixing, instead of ignoring it until it fixed itself. This wasn’t an Ancient device, this was his daughter, a girl who was emotionally overloaded and frustrated. She thought she was unloved and abandoned. 

She also had a plaster weapon encasing her right wrist. 

“Nothing to talk about.”

John prided himself in the fact that he kept his voice level and calm. “Yes, there is. And we’re going to talk about it like civilized people and we’re not leaving until this is fixed.”

“There wouldn’t be anything to fix if you hadn’t lied to me,” she growled, tugging at her cast. She was dangerously close to snapping completely. And she had the feeling that John wanted her to do just that.

“I am sorry I lied to you,” he said, pouring every ounce of sincerity he could into the statement. It was the truth; he was regretting that he hadn’t told her of the Wraith. He’d done it to protect her, shield her from the dangers of the Pegasus Galaxy and, hindsight being twenty-twenty, could see that he’d ultimately made the wrong decision. He just needed to make her see that as well. 

“Then why did you do it?” she yelled, unable to keep her temper in check anymore. “Why didn’t you tell me about something that every child in this place knows about? Why didn’t you tell me about something that could _kill_ me? Didn’t you think it was important? Why?” Tears come again, hot and embarrassing on her cheeks. 

“Because I wanted to keep you safe!” His voice rose. “I didn’t want you to be anymore scared than you already were! I wanted to keep you safe because I’m your father and that’s what parents do. They keep their kids safe. Or they try to. The situation we’re in isn’t normal. You’re not going to get hit by a car or anything here. There are no drug dealers or school shootings. There’s space vampires, for God’s sake, and I didn’t want you to feel scared. I wanted you to be _safe_ ” The last word was more pleading than anything and he felt a reciprocating wetness slide down his own cheeks. 

Her chest heaved. She wanted it to be that simple but it wasn’t. And while they were both getting things off their chest, she might as well clean out everything. “Why do you suddenly care?”

John froze. “What?”

“Why do you suddenly care? You never showed up on Earth, so why suddenly care what happens?”

The knife twisted further, gouging him deep. “I didn’t know, Alison. I told you that. Your mother, God rest her, didn’t feel the need to tell me that I had a daughter. That I had a child.” There was broken pleading in his voice; he needed her to see that it was the truth. 

“And what would have happened had you known?”

“I would have been there. For all of it. As much as I could.”

She snorted. 

“I love flying, Alison,” he said, taking a step toward her. “I love my job, and the reason that I came here was because I thought I had nothing left on Earth. I disobeyed a direct order when I was stationed in Afghanistan. I went back for my fellow soldiers, even though they died. I wasn’t in Antarctica willingly, it was because I was sent there as an example, as a punishment. And I only ended up here by accident, because I had the special gene. It was a one-way trip, and I didn’t think I had anything to lose, anything to stay for.” He took another step closer to her, trying to make her understand. “But I did. I didn’t know it, but I did. Atlantis became my home. And the Wraith? Well, I was the reason they woke up again. I was a lowly Major and in charge of the military here. And I was scared. Scared as hell.”

Ali had heard bits and pieces of the story, of the history. From the rawness in his voice he wasn’t telling her anything but the truth. 

“And…And now you’re in my life. The daughter I’d secretly hoped for, the family I wished I’d had was dropped into my life.” He laughed a little. “And I wanted nothing more than to keep you safe. And I’m sorry I lied to you. I just wanted you to be happy and safe in your new home.”

She had tears streaming down her face. “I only wanted you. Mom said…she said I was a math geek like you and I just…I wanted a dad like everybody else.” Her shoulders shook with her sobs. “And I got here and I thought you didn’t want me, that you were ashamed of me. You didn’t tell anybody…” Her breath hitched painfully in her chest. “And I thought I was going to lose another parent because you were turning into a bug and…and…then I thought you were dead because you fell down a hill and could have broke your neck and I was going to regret…”

John was within arm’s reach of her, chest aching at all the miscommunication – verbal or otherwise – between them. “I thought I was going to lose you before I really had you.” He didn’t have to elaborate; she knew he meant the Wraith. “I’m so sorry.” It was awkward at first, and it hurt his sore shoulder, but he pulled her against him, tucking her face against his chest and rocked her like he imagined Nancy had done when Ali was a little girl. 

“I just wanted a dad,” she sniffled into his chest, hands gripping painfully at his shirt. 

“Give me another shot?”

She tried to pull him closer, sobbing harder and nodding. He rocked her gently, stroking her hair and realizing that he was being given not a second chance at the whole parenting thing, but a third. The first was when he missed her entire childhood on Earth; the second their first couple months in Atlantis, and he was bound and determined not to screw this up. It would be difficult for both of them, but they’d make the awkward steps together. It was all they could do.


	7. Integration: Seeing and Believing

**Summary for the Chapter:**

> An unknown Ancient device has unpredictable consequences. 
> 
> Ali also finds friends in unexpected places.

**Notes for the Chapter:**

> Still don't own anything recognizable. 
> 
> Especially not _The Sixth Sense_ or the incredibly famous line from it.

“Why is it that David Parrish and Evan Lorne signed this before I did?” John asked, permanent marker in hand and Ali’s casted arm on his desk. 

She blushed and avoided his eyes while honestly saying, “We weren’t…talking…then.”

“Ah, gotcha,” he said, flipping her arm over to scope out the space on the bottom. He flipped it back over, ignoring her exasperated but amused huff of air. “Found it.” He took the cap off and bent over her casted arm, tongue sticking out as though he were in deep concentration. He was rewarded for his shenanigans with her chuckle. 

Things were far from perfect between them, but they were working on it. 

“There.” He straightened and put the cap back on the marker. There was some uncertainty in his eyes as she looked down. Near the back of her hand, on her wrist area was John’s chicken scratch handwriting spelling his name. In parenthesis was the word _Dad._ At the same time seeing it spelled so clearly felt odd and foreign, it also felt undeniably right. 

“Thanks,” she said, ignoring the roughness in her voice. She really needed to have some serious, non-crisis downtime or she was going to be an emotional wreck for the next month and a half. And that wouldn’t consider…yeah…she didn’t want to think about _that_ either. 

His response was to smile at her with more warmth than she’d seen in a while. She kept a firm hand on the urge to hug him. She wasn’t ready for it yet. 

“Do you want to get some lunch?” He was hesitant, unsure how far to push her. A quick glance at his watch told him it was almost one, their regular time to get lunch. Or used to be. He wasn’t sure if she’d want to continue that. Maybe once the waters smoothed out a little more they’d settle back into what they had. 

Ali distinctly remembered standing by herself, like an idiot, in the cafeteria when she and John had been having their…issues. She had no desire for a repeat performance. And, who knew, maybe they’d eventually settle back into their old routine. She kind of liked them, back then. 

“Yeah,” she said, standing. She waited for him to come around his desk, taken completely by surprise by the sudden, hard hug. She knew he did it quick to dispel some of the awkwardness of it, and she hugged him back as best she could, thumping her cast gently on his back to let him know it was okay to let go. He did, releasing her and stepping back, the color threatening to rise from his collar to his ears. Her cheeks were likewise pink. 

“Food,” they agreed together, heading for the cafeteria. 

Even after all that had happened, even after the emotional blow-up that had occurred, talking about feelings and whatnot was still difficult for him. She was back again, but she was guarded, like she expected him to pull the same thing again. Namely, she didn’t trust him like she used to. It was a mildly difficult thing to process that John Sheppard needed to get back in the good graces of his teenage daughter, win back her trust. Still, he’d do all that he could to accomplish it. He froze with a realization: he knew exactly how Rodney had felt, trust wise, after he’d blown up 3/5 of a solar system. 

“John?”

He slipped his shaking hands in his pockets. “Trying to remember my schedule for the afternoon.” She was still looking at him oddly so, without thinking, abruptly blurted, “Do you play chess?”

Her eyes lit up – almost like the time she flew a Puddlejumper for the first time. “Yeah. Do you have a board?”

_Looks like I’ll be spending my afternoon brushing up on my chess skills,_ he thought with a smile. “I’ll find one. We’ll play tonight?”

She nodded like a bobblehead gone wild and had a spring in her step all the way to the cafeteria. If chess was all it took to put it there, John made a mental note to do it more often.

* * *

John knew four moves into the first game that he was outmatched and defeat was imminent. The constant smirk on her face – his own smirk – wasn’t helping.

“Where did you learn to play?” he asked her, feeling as though he should just tip over his king and be done with it. 

“Mom taught me,” she said, deftly taking one of his rooks with a bishop. “And I joined a chess club when I was in middle school. Played with a bunch of guys who did nothing but sit around and play chess all day.” She waited for him to move, already plotting what she would do next. “Who do you play with here?”

“Rodney.” John moved a pawn, wincing when she knocked it over with a knight. “He and Radek play quite a bit. We use it to relax, especially after hard missions.” He tried not to shudder, remembering more than a few that had gone pear-shaped. He didn’t tell her that bad things happened on Atlantis, too – Ancient technology that hadn’t been properly researched and cleared and when the Marines hadn’t had enough to do to keep them occupied and got a little rowdy.

Considering what Ali knew of Rodney McKay, she didn’t think that the man would be a good person to relax around. Still, she smirked, and took John’s bishop. “Does sound like fun.” 

_McKay to Sheppard._

John reached for his earpiece, glad for the sudden break. His side of the chess board was looking a little anemic. “Sheppard here.”

There was a rush of static. _Not you, the other one._

John scowl deepened as Ali chuckled, digging her ever-present radio out of her back pocket. “Ali Sheppard.”

_”Ali, can I borrow you for a couple of minutes?”_

Ali looked from the radio to her father. John’s forehead was still a little tense. A couple of minutes to Rodney could mean a couple of hours to somebody else. Still, it would save him from having his daughter wipe the floor with him and he figured he’d need all the help he could get saving some of his dignity. Emotional outbursts still didn’t sit well with him. And when he thought about it, it was relatively harmless to let her turn Ancient technology on for Rodney. The man had a brain; he wouldn’t let anything happen to John’s daughter. He nodded.

“Be right there. Sheppard out.” She looked at the chess board. “Finish this when I come back?” 

John looked at his devastated army. “Start a new one?”

Ali scrunched up her own forehead like it was a serious diplomatic issue she was contemplating and then nodded with a smile. “Be right back.” She stood and, on an impulse, gave John a quick hug before flouncing out the door of his room and toward the nearest transporter. John sat there staring at the pieces, partially in shock, and the idea that maybe they were actually starting to get along.

But if she wasn’t back by ten he was going to go get her. That was what parents did, right? Curfews, even in unconventional circumstances?

* * *

“Dr. McKay?” Ali poked her head in the lab that Rodney and Radek usually worked in. Radek was nowhere to be found and Rodney was at a workbench, turning something over in his hands.

 _Must not have heard me,_ she thought and took a few steps into the room. “McKay?” A few more steps. “Rodney?” She paused, remembering something she’d heard John say a few times to break Rodney out of a funk or get him to focus. “Meredith?”

“What?” Rodney snapped, turning on his stool. His glare softened when he saw it was Ali. “Oh, it’s you. Took you long enough.”

Ali had enough sense to not be offended and refrained from rolling her eyes as she stepped up to the workbench. She picked up a life signs detector with a broken screen and turned it over in her hands. “Whatcha got?”

“Not entirely sure,” Rodney said, showing her the device. It was small and cylindrical with patterned grooves on the side of it. He handed to her. She ran her fingers over the grooves and turned it over in her hands. “There’s not much on it in the Ancient database, but it does say that it’s supposed to ‘protect the warriors’ or whatever that means.”

“Gotta say, Rodney,” she said, turning the cylinder over in her hands, fingers tracing the grooves, “sounds more like it would be up John’s alley than anything else.” Protect the warriors? Sounded more military than scientific. She tapped it against her palm; it was definitely solid. 

“There weren’t any overt warnings on it, it should be fine,” Rodney scoffed. He had enough self-preservation to not pull anything like that with John Sheppard’s daughter, especially since they’d started to fix things between them again. John was fiercely protective of all his people, but his only daughter first and foremost, even if said daughter didn’t realize it yet. Ali didn’t know that John had been going nearly out of his mind when they weren’t speaking to each other. 

He snorted, turning back to his laptop. “Okay. Go ahead and turn it on and tell me what happens.”

Ali was still skeptical. “You sure?”

Rodney turned a bit indignant. “If it was dangerous do you really think I’d let a teenager play around with it?” He took a deep breath and forced himself to relax. “My gene isn’t strong enough to turn it on. So that’s why I need you.” He deemed that enough explanation and turned back to the screen.

_Works for me._ She took a deep breath and closed her eyes. It was more difficult than a lifesigns detector or a transporter, but nowhere near a puddlejumper. She opened her eyes and looked at the device, the grooves beginning to glow blue.

“Anything?” he asked.

Ali swayed on her feet, the cylinder vibrating in her hand hard enough to jar her entire arm. She looked at Rodney, her vision wavering and doubling. Only it didn’t quite look right – instead of being a copy of the original, it was fainter, almost ghost-like. Pain zinged up her arm from the cylinder, smacking into her temple and her eyes rolled back in her head. She hit the ground with a thump, the device still glowing as it rolled under the workbench.

“Alison, it can’t take that long,” he said, turning to look at where she’d been standing. His eyes widened at the unconscious girl on the floor of his lab. Panic flared in his chest. “Carson! Medical emergency in my lab!” and his voice sounded only slightly hysterical. His next thought and sentence was, “OhmyGod I killed her!” And because he’d killed his daughter, John was going to kill him. 

Yup, John was definitely going to kill him.

* * *

The military man in John was calm. The parent in him was in a state of panic.

He burst through the door to the infirmary at a dead run, skidding to a halt and looking around for Carson. Beckett was nowhere to be found, currently, but Rodney was there, arms crossed over his chest and pacing, worry and embarrassment on his face. It was all John could do to restrain himself from stalking over to McKay and demanding to know what exactly had happened to his daughter. Still, it brought a roar of protectiveness to the front of his mind and a growl to his chest. He wasn’t working toward regaining his daughter and her trust for something stupid to happen and take it all away. 

It was definitely a challenge not to strangle Rodney at the moment.

Rodney stopped his pacing, eyes wide and fearful at the look of pure emotion on John Sheppard’s normally inscrutable face. “Colonel – John – I am so sorry! It was supposed to be safe, the database didn’t have any warnings, didn’t say anything about unconsciousness or any of that and I killed her didn’t I? OhmyGod I killed your daughter and now you’re going to kill me because you just got her back and I really screwed up didn’t I? OhmyGod what if Carson can’t fix this and – “

John watched as Rodney worked himself into a hysterical mess thinking that it was doing the protective part of him a favor and found the other half of him, the half that was panicking just as badly as McKay getting more and more worked up as well. He headed for her bedside, almost unaware of Rodney trailing behind him as he set up in the plastic chair by Ali’s bed. 

He couldn’t believe that he’d let her go test Ancient technology with Rodney. Rodney, of all people! He’d made a promise to himself to be a better parent and look where it had gotten him; his daughter was in the infirmary because of a damned Ancient device that had done who knew what to her. There were only so many chances he was going to get before she got completely sick of him screwing up and went back to the silent treatment routine. 

“She okay?”

John looked up to see Rodney hovering by the privacy curtain, worry and embarrassment on his features. 

“I don’t know, Rodney,” John said, his voice dripping with venom, “she hasn’t woken up yet.”

McKay paled even further. “But she will, right? She’ll wake up?”

“She better.” John fixed his friend with a hard stare, the one he usually reserved for misbehaving Marines. “And what the hell was that device?”

“I don’t know,” he said defensively, “that’s what I was trying to figure out.”

John’s eyes nearly bugged out of his head. “You let my daughter try out untested Ancient technology? What the hell were you thinking? You know how wrong things can go here, I thought you just needed her to be a light socket or something, not actually _test_ anything!” His voice was rising with his temper. 

Rodney flinched. “The database said that it was relatively harmless!”

“Relatively harmless?” John stood up and crossed his arms over his chest. “You let Alison handle something _relatively_ harmless? Jesus, Rodney, no wonder you aren’t a parent. You’d have killed your kids.” It was a cheap shot, one that John was well aware of, but it was his little girl too still and pale in an infirmary bed, not Rodney’s. And it triggered something in John that he hadn’t felt before.

“OhmyGod I killed her, didn’t I?” Rodney was a mix of indignant and horrified and then regained his stride, not to mention his snark. “Yeah, well, you aren’t exactly the World’s Greatest Dad material, Colonel.”

“You think I don’t know that?” he shot back. “At least I’m trying.”

“Like you tried with the whole Wraith thing?” McKay rolled his eyes. “Brilliant move, by the way. She absolutely loved you for that.”

“Gentlemen!”

John was aware then that his hands were at his sides, fingers curled into fists and ready to knock Rodney a good one for commenting on his barely-there but steadily improving parenting skills. What did the man know about raising kids, anyway? You couldn’t just give them something that could possibly kill them for a toy and expect to keep them both occupied and safe. But maybe it was all John’s fault for letting Ali go down and turn things on for him. He should have double checked with Rodney that it would be absolutely safe for her, that there wouldn’t be any more danger than there already was living in a different galaxy. 

Carson stormed in, shooting dirty looks between both Rodney and John. “This is an infirmary, lads, and yeh’ll keep yer voices down or take it outside.” He dared John to call him on it. “Now can ye behave?”

Sheppard nodded and sat back down by his daughter. 

“I’ve run every medical test I can think of and everything’s normal,” Carson said, taking a peek at Ali’s chart. “Except for the brain scans.”

Rodney’s eyes grew wide as saucers and he clutched at a rolling tray stand for balance, his legs nearly going out from under him. He’d brain damaged his best friend’s only child? Oh, he was going to hell for this. John was going to kill him and he was going to hell.

“Breathe, Rodney,” Carson commanded, half-tempted to look for a paper bag in case Rodney started hyperventilating. One look at John’s absolutely murderous face had him saying, “And you stay right there, Colonel.” He pinched the bridge of his nose. He wasn’t paid enough to deal with this. “Before either of yeh jump to conclusions, yeh need to listen. Alison’s brain scans are normal except for a bit of activity in the part of the brain that isn’t usually used. There’s no tumors or clots, nothing life-threatening. She’ll be fine when she wakes up, which should be shortly. As far as I can tell there wasn’t any damage done to her.”

John and Rodney relaxed. Carson took a deep breath and let it out. “I still want to monitor her when she wakes up, just to be on the safe side. Now, can I leave the two of yeh here and yeh’ll behave like adults?” Beckett could have swore he was looking at a pair of freaked out parents instead of a single dad and a best friend who hadn’t been careful enough with Ancient technology. No, that wasn’t quite right. Rodney had no doubt been careful, especially considering it was Ali they were talking about, but sometimes things happened. It was Atlantis and the Pegasus Galaxy, of course unintentional things happened on a semi-regular basis.

 

Both men had the grace to look sheepish. Rodney pulled another chair over to the opposite side of the bed. Carson retreated to his office and his bottle of aspirin. 

“I’m sorry,” Rodney said after a moment. “That was a low blow, about your parenting skills.” There was sincerity in his blue eyes and John realized that he would never do anything to intentionally hurt Ali.

John rubbed the back of his neck. “You wouldn’t kill your kids, Rodney.” His smile was soft as he looked down at Ali. “You’d be a good dad.”

Rodney colored. There was a reason he’d never had children, never had any desire. His own childhood had been less than ideal and work had always come first. He had all the children he could ever want in his niece and Ali felt like family, just like John did. He was pretty sure the rest of Atlantis felt the same about the youngest Sheppard.

Ali was pale against the infirmary sheets, pale and vulnerable. John wasn’t sure how he felt, seeing her like that. It definitely wasn’t doing wonders for his heart. 

Her eyelids finally fluttered. 

“Hey, kid,” he said, the words rolling easily off his tongue without conscious thought. He tried not to think it was a complete role reversal – she was the one in the bed this time, albeit not mutating into something strange and unnatural, and he was the one standing, worrying. After taking a deep breath, he slid his hand under hers and gave her fingers a slight squeeze.

“Hi, John.” She blinked and then squinted. Saw Rodney out of the corner of her eye. “Rodney.” He gave her a shaky smile.

“Your head hurt?”

“Yeah,” she said, breathing deep. “Did I hit it when I passed out?”

John shook his head. “Rodney said no, but he didn’t see you until you were on the floor.” 

Ali blushed and looked away. Passing out was embarrassing enough, but to do it in front of Rodney? And have John be so…calm about it? Then she noticed the twitch in his face, the way he was working so hard to keep everything – to keep his _worry_ \- from spilling over and affecting her. Was something wrong? John was the most unflappable person she knew, the most unaffected and sometimes cold person?

“Oh my God, I’m dying, aren’t I?” she asked, eyes wide and tearful. 

“What?” John went from concerned to confused in less than ten seconds. “No.” He chuckled, some of the tension leaking out of him. “No, you’re not dying.” He paused. “I’m just…concerned.” _More like worried out of my mind at the moment, but you don’t really need to know that._

She narrowed her eyes. If this was a new facet of John Sheppard it was definitely going to take some getting used to. She knew emotions were still high between them, but this was a little, almost over-the-top. So help her if he was faking it she was going right back to the silent treatment, even if it killed the both of them, literally and figuratively. 

“Why are you looking at me like that?”

“You’re concerned?”

The knife was bag, twisting once more in his gut. Her mistrust ran deeper than he’d thought.

“Yeah, I’m concerned,” he said, his tone gentle yet firm so to leave no doubt about his true intentions. “You passed out.”

Ali bit her tongue and immediately wished she could take back the words. And any apology she may have in her mind sounded fake and impersonal. They needed to stop hurting each other and start trusting, instead. Easier said than done.

He squeezed her hand to regain her attention. “Carson says that you’re physically fine, but according to your brain scans there’s parts of your brain that are really active and aren’t normally. Which is probably why you have a headache.” He smiled thinly. “He wants you to go about your day like you normally would, keep your stress level down.” 

_Stress level? What stress level?_ she thought, mildly hysterically, and nodded anyway. “And we have some chess to get caught up on.” She relaxed when he smiled. It was only then did she realize he was holding her hand and that the warm weight of his palm was both soothing and reassuring. 

It was quite nice in her opinion.

* * *

Ali leaned against the railing overlooking the Gateroom and watched the off world personnel mill around. Final preparations were being made. John appeared on her good side and nudged her elbow.

“Hey,” she said, nudging him back. “I thought you were supposed to go?”

John shrugged. “We weren’t needed and I decided to take a day off.”

Ali looked at him strangely. From what she’d heard, John Sheppard _never_ took a day off. “You have the day off?”

“Yeah,” he said wryly, “you took a header in Rodney’s lab so I took the day off.”

She flushed and looked back at the group of people waiting for the final all clear. John had taken the day off because she’d passed out. A closer, discreet look at his face, his eyes crinkled at the corners with barely hidden worry – he was truly concerned for her well-being. At the same time she wanted to balk because she didn’t trust him completely, it was nice to have someone who cared as much as he did. She moved a touch closer to him, so their elbows were touching.

John gave Lorne a jaunty wave as the man stood well-back from the Stargate as it started to spin. Lorne returned the gesture, Ali noted with a grin, and she glanced around to see what the rest of them were doing, if there were any other farewell gestures or signs. That was when she noticed it. 

It was almost like a shadow, standing behind one of the Marines by the far wall and in the exact same pose as the young man – hands clasped over his P-90 and utterly relaxed. She leaned over the railing a little further, blinking furiously. The figure on the left was as solid as she was, and the one on the right looked, well, looked more like a “ghost” than anything else. It wasn’t exactly transparent, but it wasn’t as solid-looking as a human. She glanced at John to see if he noticed anything out of the ordinary and from the even look on his face he wasn’t seeing what she was. 

That’s if she was seeing something real and not still concussed or something from the day before.

“You okay?” he asked, jolting her a bit.

“Fine,” she said automatically, her eyes glued to the shadowy, translucent figure behind the Marine as he stepped through the ‘Gate. She looked over at him when the wormhole disengaged and clarified, “Really, I’m fine.” She mentioned nothing of what she’d thought she’d seen, hoping it was simply a figment of her imagination. 

From the cold feeling in the pit of her stomach, she didn’t think she’d get that lucky.

* * *

John nabbed some turkey sandwiches from the cafeteria so he and Ali could have lunch together on the pier, the ocean stretching in front of them. He did it deliberately, hoping to calm whatever nerves his daughter was currently suffering from because he’d be damned if she wasn’t as jumpy as a cat in a room full of rockers. But she wouldn’t tell him what was wrong. She didn’t eat much of her sandwich, didn’t even touch her pudding cup, and simply sat there, rubbing her cast and staring out across the water.

“Your head still hurt?” He took a stab at what might be bothering her, hoping for some actual conversation.

Ali shook her head mutely and shivered. John automatically shrugged off his jacket and draped it around her shoulders. She started, looked away from the water at him, and smiled in thanks. She pushed her arms through the sleeves and pulled her knees to her chest. When she breathed she could smell the scent that was uniquely, uniquely her father, and it was still warm from his body heat. She put her arms on her knees and rested her cheek on them, looking over at John as he tried not to stare at her, obviously trying to figure out what was going on in her mind. 

She had to let him in sometime. 

“John?”

“Yeah?” _Tell me something,_ his mind raged, _let me in! Let me in!_

“When you turn on devices for Rodney, do you sometimes get a little…tickle, in the back of your mind? Like a residue?”

John internally jumped for joy. He kept his face carefully controlled as he nodded. “Different devices can leave different marks. Some of the newer Ancient devices, the ones created toward the end of their lifetime, are more carefully constructed and more thought through. They don’t leave as big a mark as the earlier ones.” He chuckled. “I turned on this device for Rodney one time and it literally left my ears ringing for days afterward, even though it had absolutely nothing to do with my hearing or anything. It was meant to supplement the sprinkler system in the botany labs.” There had definitely been some weird things that had filtered through the labs at one time or another, and with more sections of the city being explored and cleared, the potential for such items was increasing. 

Possibly including the thing that had knocked out Ali. 

Ali mulled his explanation over in her head. It was plausible that she was just feeling some backlash from what had happened. As much as she tried to convince herself of that, she couldn’t manage it. The idea just wouldn’t take hold. 

“That’s probably what I’m feeling,” she said, unconsciously wrapping the jacket closer around herself, the word _safe_ bouncing in the back of her mind. When she looked at John he was eyeing her as though trying to figure out how to get nearer to her to hug her or something.

_”Colonel Sheppard! Report to the Gateroom immediately!_

Both John’s earpiece and Ali’s handheld radio blared to life and it took a minute before she really registered the distress carefully hidden in Chuck’s voice. 

John swore under his breath, twisting to his feet and tapping his earpiece. “Is it Lorne’s team?”

_”Yessir.”_

“I’ll be right there. Notify the others.” He looked at Ali, pale and uncertain on her feet as she looked at him. “I gotta go.”

Ali nodded. “I’ll – I’ll take of the lunch stuff.” There wasn’t much – only what she’d only poked out and some water bottles to recycle. She smiled wanly as John kissed her on the forehead and took off at a run toward the door to the pier, most likely heading for the central tower. It was then that she realized she was still wearing his jacket, her arms wrapped as close to her midsection as they could go, trying to get that feeling of _safe_ back in her mind now that John was out of sight. Trying to get a sense of almost-normal. The jacket definitely helped.

She took the garbage inside and back to the cafeteria, gathering a few odd looks because of what she was wearing and after wandering aimlessly through the halls of Atlantis for nearly an hour finally wound up in the Gateroom on the balcony, borrowing a chair from Elizabeth’s office and setting up shop in a corner out of the way enough that she wouldn’t be a nuisance but in the right spot that she could see when the Stargate activated and everything else going on. From the rigid set of Chuck’s shoulders, whatever was happening wasn’t good. And if anybody was thinking it was odd that she was still wrapped in John’s uniform jacket that was not only too large for her but she was clutching like a drowning man clutches a buoy, they didn’t mention it. Most gave her a first or second glance and went back to what they were doing, used to her presence anytime John came or went through the Stargate. 

She was zoning out badly when the Stargate began to spin, Chuck confirming to the others around him that it was indeed Colonel Sheppard’s IDC. Ali uncurled from her chair and stood, creeping toward a corner of the balcony, still well out of the way. From her vantage point she could see Carson and a medical team standing in the doorway, waiting anxiously. 

The wormhole engaged, figures moving hurriedly through it back to the safety of Atlantis in pairs. Ronon had a Marine slung over his shoulder. Her heart kicked up until John stepped through, a clearly dazed Lorne at his side and only on his feet because of Sheppard. Ali looked at the faces as the med team intermingled with the ‘Gate teams. She found what she was inadvertently looking for as Ronon set the figure from his shoulder onto a gurney, the same shadowy figure she’d seen earlier hovering on the other side of the medical personnel. It looked up at her, flickering like a TV with an interruption in its signal. Gripping the railing hard, she watched as the translucent figure flickered a few more times and then vanished. She took a quick look around the room, desperately hoping to see it somewhere else and found nothing but solid bodies. 

The sound of a discharging defibrillator brought her back to the area below the balcony. The same Marine that Ronon had had over his shoulder, the one she’d seen the translucent figure of as on the receiving end of the paddles. 

The medic attending him rocked back on his heels, shutting down the defibrillator after the fourth try. He looked first at Carson and then at John, shaking his head sadly. 

John stood in front of the empty Stargate, hands resting on his P-90, Lorne on a gurney and heading for the infirmary, chin on his chest. He picked his head up, took a deep breath, and automatically looked at the balcony above, spotting his daughter. She paled, no doubt seeing the blood on the side of his face, still wrapped in his jacket. 

Ali gripped the railing harder, having the distinct impression that she had literally watched someone’s life flicker out before her eyes. A bloody, battle-weary John wasn’t helping, either.

* * *

Ali had a lot on her mind the next morning as she made her way to the infirmary. Carson had sent her an e-mail telling her he was taking off the cast today. While that made her invariably happy, she was also a little nervous. She was partially worried she was seeing things she shouldn’t be, courtesy of that device. Not that she would tell John – he had too much to worry about as it was without adding her drama to his workload. Besides, she hadn’t seen any other “shadows” since the day before, in the Gateroom.

She jolted to a halt when she crossed the infirmary threshold.

It was like something off the Sci-Fi channel. Three translucent Marines sat in the waiting room, absently looking at either the walls or themselves, completely unconcerned with the fact that they weren’t solid and tangible. Ali took a glance around and confirmed that there were indeed three occupied beds, each holding a Marine and hooked to some heavy-duty equipment, no doubt from the previous mission that had gone way wrong. 

Which threw her theory of her imagining it right out the window.

“Alison?”

“Hi, Carson,” she said brightly, stamping down firmly on her impending freak-out. 

“Let’s see that arm, shall we?” He led her to an exam bed, which she hopped onto without a word, extending her left arm for his inspection. If he noticed the word below John’s signature on her cast, he didn’t say anything, though the smile was in his eyes. He donned some protective eyewear, broke out the saw used to cut through the cast, and in short order the thing was off her arm. He handed her both halves, a reminder for her. She had no doubt she would never forget the events leading to the injury and the aftermath. 

She was on her way out – Carson had asked her how her head was and stared at her relentlessly for at least a minute at the mention of the word “fine” before deciding she was telling the truth – when all hell broke loose on the monitors of one of the Marines. Her eyes immediately looked at the waiting area, one form blinking and twitching, shimmering in and out of view. Her heart pounded; the shadow flickered a few times before fading completely. Once it was gone the heart monitor flat-lined. She knew he was completely gone. Clutching the halves of her cast, she fled the infirmary, intent on heading anywhere but where she might see more of them.

She wound up in Botany. 

The door to David’s “lab” opened and she stepped inside, breathing deeply of the lavender scent that was wafting through by some sort of plant to her right. She took a couple deep breaths, settling herself, and for a moment tried to imagine herself back on earth in the middle of the woods where she’d gone camping so many times with her best friends. It worked marginally and when she opened her eyes she was much less likely to spontaneously combust from stress. The more she looked around, the more she calmed. It was like the plants had a soothing effect. 

_No wonder David spends so much time in here,_ she thought. And speaking of the Botanist…he’d made it clear the first time she’d accidentally wound up in Botany that if she ever needed to talk about anything, anything at all, she could come to him. She wasn’t exactly sure what drew her to him – maybe it was because he was so young or that he was the most civilian-like of the scientists, most like a regular guy simply doing what he loved day in and day out with the occasional foray off-world. 

Maybe it was really because out of everyone on Atlantis, he reminded her the most of Earth, a place she still missed, especially on her roughest days.

“David?” she called, pulling her radio from her back pocket. She should have checked to make sure he was even on Atlantis before coming down to avoid standing there, like she was, and looking like an idiot. 

“Alison?” His voice came from the back, by some of the larger plants.

“Yeah. Up here.” She looked at the radio. John got twitchy when he couldn’t find her, an after-effect of her first trip off-world. Cradling the two halves of her cast, she turned the radio off. She didn’t want to be found, not for this conversation. And she didn’t want listen in, if she accidentally pressed the button. 

“Hey, you got yours off, too,” he said, appearing around a row of potted plants and holding up his own cast-free arm. 

“Just now,” she showed him the pieces with a wave. She placed them on the table with some empty pots, along with the radio. “Can we talk?”

David didn’t like the look in her eyes, the fear and uncertainty. “Of course.” She might have been John Sheppard’s daughter but he knew damn well that she was considered a little sister by most of the base. He was no exception. “How about back by the Earth plants? The spider plant is almost ready to start growing babies.”

She nodded, following him back to the area where he kept the plants that they had brought with them from Earth. David had a regular houseplant in a good-sized pot that, when it was ready, would grow off-shoots that could be regrown on their own. She perched on a stool, picking up the pot and feeling the terra cotta under her fingers. Her mother had tried to garden a bit, especially in the spring. Neither woman had been good at it.

“What’s up, Ali?” David asked, pulling his desk chair from his office in the back so it didn’t feel quite like a Dr. Phil show and more like two friends talking.

Ali twisted her hands together, staring at the floor. She reached up and took her hair out of his ponytail, shaking it out so she could hide behind it, if need be. 

“Ever have anything weird happen?” she asked, looking at him. From the look on his face, she realized she needed to rephrase her question. Asking someone who had lived in Atlantis that long if he’d had anything weird happen was like asking if the sky was blue. She chewed her bottom lip. “I mean – Have you ever had a concussion?”

David winced. “On more than one occasion.” Going into the field with Evan’s team, though they were careful, still held risks. 

“Okay, so, do you know when you have a concussion…Sometimes you see things?” She drew her knees up as far as possible without falling off the stool. “Like, double vision. Blurry figures.”

He leaned forward, mostly to hear better since her voice had gotten quiet. Scared.

“I’ve been seeing things.” She swallowed hard. “I’ve been seeing blurry figures, ghosts, but…they’re not dead when I see them.” 

“What do you mean?” Thank God for the Pegasus Galaxy because he was not only completely prepared for her to go _Sixth Sense_ on him, he was actually expecting it.

Ali took a deep breath and breathed it out slow. “Yesterday. Before Evan left, when everybody was in the Gateroom, I saw this shadow by a Marine.” She paused, searching for what she wanted to say. “It was like I was seeing double, only the second one didn’t look solid. It was faded, a little blurry. But it was _there_ and it followed him through the ‘Gate. And it was there when they came back, only…the Marine that it belonged to wasn’t so good. Carson had to use the paddles.” She brushed her hair behind her ears. “And…the second one….the second one just flickered. Flickered and waved, like a, a, a TV signal that’s been interrupted. And then it flickered out completely. And Carson couldn’t bring him back.”

David swallowed the lump in his throat. The only tentative conclusion he could draw from what Ali was telling him was that she was somehow seeing people who were going to die, before they did it. Which was more than absurd in reality, but, throw in an Ancient device that’s been sitting on a shelf for a few millennia and there was the possibility of a disaster. 

“Has it happened again?” he asked. Once could be explained as a freak accident, but twice in as many days would be solid proof that something was wrong.

Her fingers rubbed her forearm, like she was automatically searching for the cast that wasn’t there anymore. “Yeah. I went to get my cast cut off and there were three of them in the waiting area, just sitting there. When I left, one of them started to flicker. When it faded the machines went nuts.” She looked at him, her eyes unreadable except for the moisture in the corners. “I literally ran from the infirmary.”

It didn’t take a rocket scientist to see she was scared. And it didn’t take a genius to know what his next question was invariably going to be. 

“Have you told John?”

Ali’s head snapped up. “No.” She started to shake her head. “No. I – I can’t.”

David frowned. “Why not?”

Her lower lip wobbled. “He’s…He’s got so much to worry about. He just lost, what, at least two men?” She wasn’t stupid – she’d seen the look in his eyes that said the loss of life wasn’t sitting well with him. “I can’t tell him. I can’t add more to what he’s already got to worry about. I just can’t.” Her voice was pleading with him. John had so much to deal with, being the military commander, losing two soldiers and dealing with anything else that happened to come his way that she couldn’t knowingly add to his pile of stuff. She couldn’t add something that she wasn’t sure he could even fix to his list of things to worry about it. She’d deal with it on her own. “I can’t tell him.” She said it firmly, looking David in the eyes.

“Okay,” he conceded. “It’s your decision, but I really think you should.”

She shook her head stubbornly. “I can’t.”

They both jumped as a new voice called David’s name from the front of the lab.

“Evan,” David muttered, a flush coloring his cheeks briefly. He’d completely forgotten that Evan was coming by and having lunch with him, since he was recovering and didn’t really have much else to do except paperwork. 

“David?” Lorne called again, making his way toward them. 

Parrish gave Ali a small, sheepish smile and called, “Back here.”

Though she hadn’t shed any tears, Ali wiped under her eyes anyway, hoping she didn’t look as shaken as she still felt. Talking about it had only served to make it more real, not less creepy. 

“Hey,” Evan said as he rounded a row of plants. “Hey, Ali.” 

She clutched at the terra cotta pot still balanced in her lap. “Hi.”

Lorne’s eyes took in the set up and would have held up both hands if one arm hadn’t been in a sling. “Am I interrupting something?”

Ali blushed furiously, the color stark against the paleness of the rest of her face. “Just talking.” She looked up at Lorne; he had a brilliant black eye, a butterfly bandage across his eyebrow, and another on his hairline. “You look better.”

Evan grinned. “Thanks. I feel better. Carson’s good drugs.” 

She smiled and looked at the plant in her hands. She didn’t hear David come back until he called her name.

“Do you want to have lunch with us?”

She looked between them, feeling as though the terra cotta beneath her fingers was the only thing keeping her grounded. A quick glance at her watch told her it was almost one. Normally she’d have lunch with John but considering he had a slight concussion – and the day off – it was a good chance that he hadn’t rolled out of bed yet. If that was the case, she surely wasn’t going to call him and wake him up, either.

“Okay.” She set the plant down and hopped off the stool. 

Evan smiled and headed for the door, scooping up the pieces of her cast with his good arm on his way out. David hung back while Ali got her bearings again, and she looked at him expectantly. There was something he wanted to ask, and she was pretty sure she knew what it was. 

“You want me to tell you if I see another shadow, don’t you?” she sighed. This was going to get pretty old, pretty quick. She knew, logically, that if she told John or Rodney, maybe even Radek, then they could all work together on solving this and getting her back to normal. Or at least to the point where she wasn’t seeing people who were going to die before they died. 

David nodded. “There’s nobody scheduled for off-world today, but you never know.” 

What he really meant was that he wanted to make sure it was no fluke. To verify that what she was seeing was, without a doubt, real. Then it would be a question of how many bodies piled up before she told John. Or before it ripped her apart emotionally.

* * *

She made it forty-nine minutes in the cafeteria before she saw one. Of course, David, sitting next to her, felt her stiffen.

“Where?” he murmured, ignoring Evan’s curious gaze.

“By the fruit.”

“Anderson,” David muttered, immediately wondering how to tell him to be extra careful without drawing attention to the situation. 

“Anderson?” Evan repeated, completely lost to the entire conversation and only semi-successful at eating left-handed. 

Ali pushed her pudding cup away, her stomach souring. She hated this, she honestly did. Even worse was the quiet conversation that David had with Evan, explaining everything without crucial details. From the look in Evan’s eyes, he wanted those details but would wait. He looked sidelong at Ali and she realized, from the mirrored expression in his eyes, that she must look absolutely miserable. No doubt he would be on her now to tell John. Didn’t they understand she couldn’t? That she couldn’t burden him further with something that might turn out to be a fluke? Something that might turn out to be nothing tangible, nothing real? He didn’t need to worry about her, he had enough to worry about.

No matter what David would say, she couldn’t add more to John. She couldn’t. Not after the Wraith fiasco.

* * *

Corporal Harris Anderson died when an abandoned section of the city he was exploring and clearing with a group of scientists crumbled, the floor literally giving way beneath his feet. Carson said it had been quick and painless; a broken neck.

Ali heard the news and fled back to her room, back to her balcony where she wrapped herself in a blanket and tried to lose herself in the noise of the waves against the city. She had to tell someone. She had to. She couldn’t live with the guilt that was eating her alive from the inside out that she had known and could have done something, could have told John, rather than a cryptic warning of “Be careful” from Evan earlier that day. No, what she really needed was help, as loathe as she was to accept what David had told her before. 

She needed to tell John.

* * *

“John?”

John looked up from the seemingly unendless pile of paperwork on his desk and nearly did a double-take. He hadn’t seen Ali in a day or two, since coming back from Lorne’s rescue mission, but there was something drastically wrong. There were circles so dark under her eyes they looked like bruises and she was…scared. Maybe terrified was a better word. Terrified of what he wasn’t sure, but he would most definitely be finding out. 

“Alison,” he said, remembering at the last moment to keep his voice calm and neutral. The last thing he wanted to do was spook her anymore than she already was. “What’s up?”

She entered his office, making a beeline for the chair, and the door shut behind her. When she was curled as much as possible in the chair across from his desk, and looking so much younger and more vulnerable than he’d ever seen her, even when the pain of losing her mother was still so fresh, she hugged her knees to her chest and said, in a quiet voice, “I think there’s something wrong with me.”

_Obviously._ John put down his pen, letting her know that she had his full attention for whatever she was going to talk about. 

Her lower lip wobbled, a blush creeping up her cheeks. Why was this so difficult? Why was it so difficult to tell her father, a man who was still partially a stranger to her, that she was seeing people before they died? That this was a byproduct of what had happened in Rodney’s lab and that it was scaring the living crap out of her and she wanted it fixed? Why was it so difficult to tell him she was scared?

And then she knew. It was hard for her to seem vulnerable in front of him because that meant she would have to let him in emotionally, let him step into more of a father role with her than an outsider who shared half her DNA. And for some reason she was terrified of that. 

“What’s going on, Ali?”

“I’m seeing things,” she admitted, settling on getting everything out like you’d rip off a Band-Aid – fast, so it wouldn’t pull out all your arm hair. 

John knew this went completely above and beyond the usual Pegasus creepy and into something far more dangerous. He stood and came around to the front of his desk, kneeling on the floor so that they were approximately the same height. Slowly, in case she spooked easily – and she looked like she might rabbit out of his office at any moment – he brought his hands up and took hers between his. He ignored that they were like icicles. “What kinds of things are you seeing?”

Ali balked visibly. The only thing that was keeping her somewhat grounded was his warm hands around hers. That alone told her that she could say something completely off-the-wall and he’d be completely okay with it. A closer look at the tension around his eyes revealed that he was worried. Worried and concerned. 

“I’m seeing…I’m seeing people who are going to die before they die.” That simple statement took more effort than she would have figured. 

And what John didn’t do shook her more than what he could have done. 

John didn’t laugh at her, tell her it was nothing, tell her it was her imagination and that he had work to do. Most of all, John didn’t tell her he didn’t care. He didn’t tell her she was stupid, that she was worried for nothing. He didn’t do anything but squeeze her hands reassuringly and ask, “How long?” There was no doubt in his voice, no skepticism, and she bit her lip as tears flooded her eyes.

“Since – Since Rodney’s lab.” She couldn’t believe that he wasn’t upset. Couldn’t believe that he was completely fine with it, that he believed her.

“Since..hey, hey it’s alright,” he said, noticing her distress and not fighting the rising parental need in him to comfort his child. He’d been having a lot of parental “urges” over the past few weeks (since she’d arrived, really, when he found out he actually had a kid) and he’d learned that it was best to simply go with the proverbial flow. Even if they both still sucked at talking about emotional things. He kept one hand on hers and reached with the other to wipe the tears steadily leaking down her cheeks. “Hey, now that we know what’s wrong we can fix it.” Her hazel eyes - _his_ hazel eyes – stared back him, huge and fearful. 

“Really?” she dared to ask in a small voice.

“Really,” he said firmly, trying to do his best to reassure her. They could fix this. Between him and Rodney they could fix this. Well…between him, Rodney, and Carson, they damn well _better_ fix it.

* * *

Ali sat on a stool in Rodney’s lab, the device that had knocked her out hooked to a machine, Rodney tapping away at his laptop as John literally looked over his shoulder. Why Elizabeth wasn’t in there, hovering as well, was a bit of a mystery.

“I’ve searched every database I know and I’m getting the same things – protect the warriors.” Rodney gave John an exasperated look. He really was trying to figure this out. 

“Okay,” John drawled. “Nothing else? Nothing she’s supposed to do? No instructions?”

Rodney rolled his eyes. “If it came with an operator’s manual, Colonel, then I wouldn’t have needed your daughter.”

Ali tuned out most of the bickering at that point, knowing it was a way for them to blow off some concern. She couldn’t help but keep thinking, “protect the warriors” over and over, until it had become a sort of mantra in her head, sure it was the one clue to cracking this damn mystery.

Then it clicked.

The device was a warning system, designed to prevent casualty, not confirm it. It was to allow for added safety and security, not drive her insane. It was to make sure that those who would be in immediate danger knew it, and knew to be extra careful. She was immediately off-handedly reminded of the Sci-Fi show _The Sentinel_ in a way, and while that was humorous, it didn’t really help her situation much. She didn’t have almost supernatural senses. 

“I got it,” she muttered. Then she shouted it to get John and Rodney’s attention. She could see the gears turning in the scientist’s mind as she explained, glad for John’s comforting hand on her shoulder – it helped keep her grounded. 

“Yes, yes,” Rodney said when she was finished, snapping his fingers together in excitement, “which means that to satisfy this thing you need to save the next person you see who’s going to kick it.”

“Save them?” she asked. Save them? She couldn’t save herself some days even if she’d tried, but she had taken lifeguard training in high school the year before, in gym class. Still, she didn’t expect to be saving anyone, though Atlantis was, appropriately, water-bound. No one did much swimming. 

“Well, you don’t have to personally save them bodily harm,” John said quickly, seeing Ali’s look of absolute panic. “We’ll help you.” 

She knew John meant well. Somehow, she wasn’t completely reassured. The expiration of her lifeguard certification didn’t help.

* * *

Ali sat in the cafeteria, playing with the tag on the tea bag and just observing. It was the middle of the afternoon, after her customary lunch with John. Atlantis was a great place to people-watch. Considering she also had an ulterior motive of sorts, it was helping her sort through the scientists and military. Rodney was confident that the next one to show up would be military. John agreed it was logical, which had prompted Rodney to make a _Star Trek_ comment.

With so much time on her own to think it was really beginning to allow the changes in her life to settle in. She was becoming more adjusted to being with John, beginning to allow him to slide into a father role. And it scared her. It scared her that she could allow him to slip into her life, to soothe the hurt left by the death of her mother. She missed Nancy fiercely (it couldn’t be helped), but John was still so unfamiliar to her.

Honestly, she was scared to let him in. Scared to let him be her father.

She pushed her mug away from her and rubbed her eyes. Why was life so damn difficult? When she looked up she froze, her mind going blank. A Marine had walked in, an ethereal shadow in his wake. He grabbed a sandwich and some water, and for the first time, the shadow mimicked him to a degree. Ali stood, grabbing blindly for her mug and nearly spilling it on herself, she hurried to the dirty dish station, her eyes on the Marine.

“You okay, Ali?”

She looked at Mya, the woman who kept an eye on the food line to make sure it was always stocked. She always said hello to Ali. Always said hello to everyone.

_Everyone._

“Hey,” Ali said, “do you know him?” She pointed to the Marine she was watching.

Mya shrugged. “That’s Sergeant Stackhouse.”

“Thanks.” She tugged her radio out of her back pocket, moving to follow Stackhouse from the cafeteria. “Ali Shep to John Shep.”

_Go ahead._

“Got one.”

_Who?_

“Stackhouse.” She stumbled over the name.

_”I’ll get him. Meet us in my office._

Which would be the hard part. Convincing Stackhouse that he might die soon, but not to worry, Ali was going to save him.

They weren’t going to convince him. Not at the rate they were going. Ali shoved the thought out of her head and moved toward John’s office, taking her time and hoping John could make it clear to Stackhouse that they weren’t going nuts. She fought the derisive snort threatening to get loose; it wouldn’t do anything to help her.

Wouldn’t help the cause, anyway, but might help her emotional stability. And sanity.

She hadn’t moved to wave a hand over the chime and the door opened automatically. She smiled apologetically with a shrug.

John waved her in. “Sergeant, this is my daughter, Alison.”

Ali held out her hand when the man in the chair turned. 

“Ali, Sergeant James Stackhouse,” John continued, moving a stack of papers off the corner of his desk.

“Nice to meet you,” she said, moving to the spot he’d cleaned. She gave her father a smaile and perched on his desk. He rubbed her back briefly to let her know he was there for her.

“So,” Stackhouse said cheerfully, “I’m going to die soon?”

The younger Sheppard almost fell off the desk at his blunt question. Her lips moved but her brain hadn’t caught up enough to form an adequate response. John rubbed her shoulder. 

“Sorry,” he said, chagrined, “I can be a bit blunt.” He looked at her, a slight tilt to his head. “You weren’t sure I was going to believe you.”

She flushed darkly as he made it a statement, not a question, reminding herself that she really needed to remember that the people of Atlantis dealt with strange on a daily basis. It was normal for them. And they supported one another as a family. John’s family. Her family.

If she let it.

“So,” John said to break the tenseness, “the idea that we came up with is that Ali’s going to kind of be your shadow so she can monitor your…other…shadow.”

“I’m grounded?” Stackhouse did his best to not sound disappointed. 

Ali did her best not to quip, “Hey, that’s my line.”

John nodded; Stackhouse gave a half shrug. “Okay.”

The unspoken “take care of my kid” hunt between the Marine and his CO. Ali could almost see the words in the air they were so tangible. Then she realized she was going to spending a _lot_ of time with Stackhouse. Did they have anything in common, anything to help pass the time together? Or were they going to end up sitting in the cafeteria, staring at each other?

“Alison?”

“Ali,” she said automatically, standing when he did. She must have missed John doing whatever it was that he was supposed to do militarily to let him go.

“Jamie,” Stackhouse said, “or Stacks.”

“Mini Shep,” she grinned, waving goodbye to John as she left his office. “Little Shep. Either one.”

Jamie grinned. “So, do you play chess?”

Ali grinned ferally. Maybe this wouldn’t be so bad.

* * *

Roughly ninety-three chess games later – in which she’d won ninety-two of them – she was beginning to rethink her previous statement. Three days after Jamie had learned he was going to either die or be saved by Ali, the two of them were having a late lunch – John was in a meeting, scheduled to gate out at eight the following morning – and she was starting to wish she’d never touched that damn device.

Especially when the conversation turned a little awkward.

“Do you mind if I ask you something?” Jamie said.

Ali wrapped her hands around her mug of tea. Inwardly took a deep breath. “Sure.”

“Why do you call your dad by his first name?”

Whatever she’d been preparing for, _that_ wasn’t it.

She couldn’t fault him for asking; lots of people were probably wondering the same thing, only didn’t feel as though they knew her well enough to ask. Or figured it wasn’t their business. Considering that she’d spent the last three days roughly glued to Jamie’s side, their conversations covering a wide variety of topics, it made sense for him to ask. However, it didn’t mean that she had an answer.

“I don’t…I don’t call him that because that’s not…” She wasn’t sure how to say it without sounding like an absolute bitch or an ungrateful brat. But it was the truth, something her mother had raised her to tell. Even if it kind of hurt. “Don’t take this the wrong way, but I don’t call him ‘dad’ because I don’t think of him that way. Not yet, at least.”

He sat back and looked at her, obviously waiting for an explanation. 

_And I haven’t even explained this to David yet,_ she thought. She looked into her tea mug. _I’d better just start at the beginning and hope he understands._ She took a deep, fortifying breath, stalling as she tried to organize her thoughts.

“I’m going to start at the beginning,” she warned. She took another deep breath. “I grew up in Colorado with just my mom. It was nice, great, even, but I was missing something. She’d told me who my dad was, so it wasn’t like I didn’t know, and she told me he was in the military.” Her smile was a little brittle. “We had a photo of him in his dress blues on the mantle.” She’d brought the photo with her when she’d moved from the only home she’d ever known. She’d taken all the photos – they were in a storage unit in Colorado Springs, paid for by the Air Force. She was going to ask John to have them shipped to her. If anything, it would help her and John connect.

She played with the tag on the tea bag. “I remember being eight, in elementary school, and it was June. Our art project was a card for Father’s Day. I didn’t know what to do. I was the only kid in my class, besides this guy who was an orphan, who didn’t have a dad. That was the only thing I wanted back then. I wanted to be like the other kids and have a dad.” She shrugged, trying to make him think it hadn’t hurt the way it had. The way the other kids had teased behind her back. “When I got older, because my dad wasn’t around, he started to feel less like my parent. He started to be John. It – It hurt less, I guess. Because he became a person, not a family member to be hurt by. I got used to realizing that my other parent was only that in the name of the position. I didn’t recognize him as my dad. He’s John.” She looked at Jamie, amazed that she was crying. “Don’t get me wrong, I’d like to call him dad, and I’m sure he’d like me to do it, too. But I’m not ready. One day I will be, but right now I’m not.” There was a sadness in her eyes. It really hurt that John wasn’t “dad” yet but she comfort and stability that went with the title was absent for her.

Jamie looked at her and after several moments in which neither of them spoke or even looked at each other, he cleared his throat.

“I grew up in Indiana,” he said. “I have both my parents.” He looked at the table, a little guilty. “I don’t know what you went through, especially losing your mom, but if I did, I think I would feel the same way.” He gave her a small smile. 

Tears pricked her eyes. He wasn’t judging her. Or her situation. Or her reaction.

“Hey, hey, you okay?”

This must be what it was like to be surrounded by understanding people; a family. 

“Yeah,” she said. “I’m great.” And she wasn’t lying this time. 

Jamie grinned. “Cool.”

“If I was in better shape, I’d say let’s go running,” she joked, downing the rest of her now-cold tea. She wasn’t going to kid herself – there was no way in hell she would be able to keep up with a Marine. Even if he went at her pace.

He chuckled. “There’s this pretty cool Ancient game room thing in a part of the city Markham’s team cleared yesterday.”

“I was going to suggest a movie, but hey, that sounds a little more fun.”

Jamie led the pair of them away from the main hub of the city. Ali noticed how quiet it was, which was why her head beginning to hurt didn’t make any sense. It was starting to pound behind her eyeballs, the same spot that had hurt after touching the device. She rubbed her forehead; the pounding increased.

“Jamie?” She had to tell him. This had to be a warning.

“I think this is it,” he said, misreading her tone. “Danny’s crap with directions, but I’m pretty sure,” He waved his hand over the panel to open a door; Ali’s head spiked in agony.

A beam of blue light shot from the panel to Jamie’s hand, lacing up his arm and diving into his chest. He looked at her, flexing his fingers with an astounded smile. Ali smiled tentatively back at him, ignoring the pain in her head and hoping her heart wasn’t going to bust out of her ribcage. He was okay…he had to be..

His eyes rolled back and he hit the floor with a thump.

“Jamie!” she screamed. She panicked for a moment and then it came flooding back to her in a jumble, all the drills and tests, the Red Cross guidelines. She dropped to her knees and rolled him onto his back, one hand fumbling for her radio, the other reaching for his neck. There was a pulse, amazingly, and as she looked for signs of breathing, brought her radio up. “Carson!” Radio etiquette had clearly gone out the window.

“Alison?”

“I’ve got a medical emergency!” Her head was going to pop off, that was a given. The question was if it would wait until help arrived. “Stackhouse is down, he’s not breathing!”

“Shite!” Carson swore, shouting instructions in the background for supplies and personnel. “Do yeh know where yeh are?”

“No,” she said, “but I was a lifeguard.” In another galaxy. In another lifetime.

“Start breathing,” Carson commanded and Ali dropped the radio in order to tilt Jamie’s head back. She hesitated only briefly. In all her sixteen, nearly seventeen, years of life, she’d never kissed a boy. Jamie was her first and she was doing it to try and save his life. She pinched his nose without a second thought and started to try and literally breathe for him. Out of the corner of her eye she saw his shadow kneel across from her.

She reached the end of the cycle, did another round of ABC’s and her heart sank; she’d lost the pulse. Shaky hands found the spot on his chest and she pressed, mindful of the ribs under her.

“Come on, Jamie,” she whispered, “come on.” She looked at the translucent figure in front of her, determination in her hazel eyes. “You can’t have him,” she told the figure. “You can’t.”

Jamie’s shadow shrugged as though to say what happened would happen. He flickered. Her head was seriously going to divorce her shoulders. 

“Come on, Jamie,” she growled. Something gave beneath her hands. “Shit.” Now there was the risk that something was broken. Something else to go wrong when everything was already heading to hell.

“Ali!” 

Even in her panicked adrenaline-filled world, she’d recognize that brogue anywhere. “Carson! Hurry!” She breathed into Jamie’s mouth again. “Hang on, Jamie, real help is here.”

Carson, Ronon, and a host of medical personnel and equipment flooded the corridor. Someone moved her away from Jamie, another hooked an ambu-bag mask over his nose and mouth. Ali stumbled to her feet, the heel of her hand pressed to her forehead, and looked on with wide eyes. She was supposed to save him, damn it, save the warrior. She felt more than she saw someone step up to her; she knew who it was instinctively, turning blindly into John’s warmth. He put his arms around her as the whine of the defibrillator filled the hall. She turned her head to look, she had to; Carson hit Jamie with the machine and the translucent figure flickered. The figure faded out then in. Ali’s eyes watered. How many more were going to die before they fixed this? Before they saved someone as they were supposed to save Jamie?

How long before her head exploded?

She watched, horrified, as the figure flickered and finally winked out. John stroked her hair, murmuring soft words to her as she buried her pounding head into his chest with a sob. She’d killed another one.

“I’ve got a pulse!”

Ali whipped her head around so fast John thought she was going to give herself whiplash. She laughed shakily in relief. She hadn’t killed him. She’d saved him, and she could let it go. 

This time, John caught her before she could hit the floor.

* * *

Ali opened her eyes slowly, blinking away the blurriness. The rough sheets under her fingertips told her she wasn’t in her room, the bright white walls and sterile smell in her nose hinted at a medical place. John asleep in a hard plastic chair by her bed confirmed infirmary.

“John?” she said softly, surprised her voice worked. She was also surprised that her head didn’t hurt.

He jerked awake. “Hey.” He rubbed a hand over his face and scooted closer to her. “How you feelin’?”

She blinked. Her head didn’t hurt. Nothing hurt. And there was no hint of a pre-dead translucent figure anywhere. “I’m good.” She smiled. “I’m real good.”

He moved a strand of her hair from her eyes. Hazel eyes they shared. “The device shut down once Stackhouse had a pulse again. It’s locked up, in Rodney’s lab along with some other dangerous things.” He smiled tenderly. “It’s over.” And he was pretty sure he was as glad as she was, considering he wouldn’t have to see his child in pain anymore and not know how to fix it.

Ali nodded, pleased that the most recent nightmare had come to an end. But one thing bothered her a bit more than anything. “Why did it take you so long to find us?” It had seemed like forever until Carson had showed up, and at the time, she was pretty sure that Jamie didn’t have forever.

“It had only felt that way,” he said. “We got there in under four minutes.” He took her hand, a reversal of the way they had been when John had been morphing into a bug, a fact that was not lost on either of them. Still, he could see some confusion in her eyes. “Your emergency trumped everything, including the rest of my meeting and my mission that was scheduled for today.” There was a silent promise in his eyes that it would always be like that, whether or not she believed it should be. “And it always feels longer than it is.” He shrugged a bit; she mirrored the movement.

“Adrenaline,” they said together, ending in a chuckle.

“How’s Jamie?” Ali asked after a moment of comfortable silence between them. 

“Well,” John said, moving around the curtain on her left. “Ask him.” He peeled it back. Jamie lay in the bed next to hers. He turned his head and smiled.

“Hey,” she said, not able to stop the grin from surfacing. It was probably a miracle they were both still alive, Jamie more so than her, but still. A miracle.

Or some really, really dumb luck coupled with outdated lifeguarding lessons, on Ali’s part.

“Howdy.” He didn’t move much; she’d cracked a rib doing CPR and it hurt to move, even a little. He waited until John moved to the other side of the bed and into his chair before saying, “Thank you. Carson told me that if you hadn’t done what you’d done…” He trailed off. She could see both what he was trying to say and the sincerity with which he was saying it. She understood completely. 

“You’re welcome,” she said, hoping the strength of her emotion got through. She snuggled into her pillow, grinning at a sudden thought. “You owe me a movie, by the way.”

Jamie grinned in return. “That I can do.”

John had settled into his chair like it was his job, feet propped on the bed rail, content and only slightly concerned. Things were moving toward normal, and his relationship with his daughter was a little firmer. If they could have some time between one crisis and the next – 

Rodney burst into the infirmary, shrieking about food poisoning, and making a beeline for Carson’s office.

Ali grinned, eyes drifting shut. Definitely heading for Atlantis normal.


	8. Integration: Coup de Grace

**Summary for the Chapter:**

> A rewritten version of events from _Coup d'Etat_ and _Grace Under Pressure_

After Carson gave her a clean bill of health, Ali felt the need to sort of decompress. She therefore headed to Botany, and David. She was kind of sure that he would have heard what had gone on with Jamie, and was probably waiting for her. Rounding the final corner, she stalled, and then stepped back.

David and Evan were in the hallway, standing a bit close to each other. A bit close meaning chest to chest. And the last thing she wanted to do was intrude.

She’d had the suspicion for a while that the two were closer than regulations allowed, but if it was something she’d learned, sometimes regulations were meant to be ignored. And, as she knew all too well, life was short. Way too short.

Ali peeked around the corner, smiling a bit when she caught the tail end of their goodbye kiss. Taking a few steps back and hoping it looked natural, she stepped around the corner and nearly ran into Evan.

“Hey,” she said. She noticed he was dressed to head out.

“Hey,” he smiled. “Heading to see David?”

She nodded. “It’s been an interesting couple of days.” Which they both knew was an understatement. Her eyes turned serious. “Be careful.”

Evan’s eyes went a bit wide. “Are you…?”

Ali shook her head. “Not anymore.” Thank God. “Just…friend to friend.”

“Will do.” He smiled and continued on his way.

She entered Botany, immediately looking toward the back. David was tinkering with some of the Earth plants, his expression carefully neutral. Ali waited until he noticed her to smile and wave. His smile wasn’t steady. He was worried and trying very hard not to show it.

“Heard you’ve had an interesting time lately,” he said with a wry smile. His eyes turned serious. “But I am glad that you told John about what was going on. He believed you completely, didn’t he?”

She blushed, honestly wondering why she’d been afraid to tell him. Just like David had said, he’d wanted to fix things. And he had. She was really glad David had refrained from uttering the words “I told you so.” 

“So did Jamie,” she added, finding her stool and settling on it. “And I didn’t tell him.”

David handed her the terra cotta pot. It was her grounding mechanism because it reminded her invariably of Earth. She looked at David; slightly shaking hands, this look on his face that said he had something on his mind. She wanted to be an ear for him, the way he was for her. To do that she’d have to let him know she knew, since it was something he probably couldn’t talk about openly. Considering Evan was military, that had probably closed off what little options they had left.

Ali wanted to be an option for David.

“I know,” she said softly, figuring the best way was to be blunt.

He paused. “What?” His eyes narrowed shrewdly.

“I know,” she said, looking him in the eye, “about the two of you. Accidentally. Just now.” She thought on that and pieced all the bits together, all the times they were in each other’s company, all the light touches, the looks. “Well, put all the pieces together just now.”

David looked as though he were going to panic and she added quickly, “I’m not going to say anything.” His eyes were still bugging out. “Really. David, I’m not going to tell. I just – You listen when I need to get things off my chest and you look like you need someone to do the same for you.”

“You’re the Colonel’s daughter,” he croaked, as though that answered everything.

“I know, but he can’t ask right? Isn’t that the way it works?” She looked at him earnestly. “We don’t talk about this stuff anyway. Trust me.”

He looked at her closely and then sagged. She smiled encouragingly as he went and got his chair. It was kind of nice, this role reversal. She seemed to be doing that quite a bit lately.

“I worry,” he said, flopping into his chair. “It happens. There’s always the chance that when you go through the ‘Gate you don’t come back. You understand that. I don’t normally worry this much but something feels off today. Feels funny.” He shrugged. “And I guess that’s what’s really bothering me.”

Ali felt the terra cotta beneath her fingers and thought of what to say. She knew what it was like to worry about someone going out and maybe not coming back. John was on the flagship team. If anyone was more likely to not come back, it would be him or one of his team. But Evan had just as much potential to the do the same.

She remembered what someone had told her, what she’d heard and what she’d eventually come to realize – John would always do his best to come back to her, now that he had her. The same would be true for Evan and David.

“He’ll come back to you, David,” she said, “and do his best to make sure he comes home.” She looked at the plant, softly adding, “John will always do his best to come home to me.” That much she knew was true.

David stood, taking her by surprise and hugging her. With the plant squished between them, she hugged him back just as fiercely. She knew what it was like to need something to hang onto.

* * *

She knew something was wrong when John didn’t meet her for lunch and didn’t call on the radio to tell her. Jamie Stackhouse gave her some company as she sipped her tea, looking like he hadn’t previously been hit with a defibrillator earlier in the week. If anything, he looked more alive, if that was possible. Ali wondered how he pulled it off.

“I’m sorry, Jamie,” she said, “but I gotta go see John.” She didn’t even try to articulate that something felt wrong. He shrugged, said he understood, and she left, taking her tea mug with her. When she got to his office and waved her hand over the panel, she almost dropped her mug. It wasn’t the sight of John with his head in his hands on his desk that made her stop.

It was the pile of silver on his desk.

Ali sank into the chair, placing her mug on the corner of his desk he usually kept clean for her. She looked at the pile and her heart sank immediately to her ankles. The top tag was one she recognized. 

Air Force Major Evan Michael Lorne.

John picked his head up, his hazel eyes wide and sad. Carefully, he picked the tags off his desk and put them in the top drawer.

“Carson,” he paused, clearing his throat that seemed thick and unlike him, “Carson’s doing an autopsy. I’m sorry I missed lunch.” He trailed off, looking at the drawer. 

“It’s okay,” she said. This was more important, and they both knew it, even as rocky as things still were between them. “Dinner?”

He swallowed, not sure if he was going to be able to eat. He nodded anyway; if he couldn’t eat, then he could at least keep her company. Standing, he kissed her forehead on the way out.

Once he’d left, Ali moved around to his chair, sinking into it and the warmth leftover from his body. There were rough draft beginnings of letters to spouses and families. Addresses on Earth where the tags would be sent. 

Dog tags went to spouses. She knew this from stories from her mother about the early days of her and John’s marriage. It had been her nightmare to open the door and see servicemen with a folded flag, dog tags piled on top. Ali wiped her eyes and looked at the desk drawer. 

Spouses.

David was as much Evan’s spouse as anything, from the way they interacted. It spoke of a long-term, loving relationship, much the way Ali’s grandparents, married fifty years, had spoken before they’d died.

She opened the drawer, gently untangling Evan’s tags from the rest and holding them in her palm. It hadn’t quite hit her that he was gone, that he wasn’t coming back. Kind of made her earlier words moot. But David had to know that Evan had done his best to come home.

Ali wiped a tear from her cheek and closed the drawer. This was going to be hard, but it was something she needed to do. 

_Like father, like daughter,_ she thought ironically, pocketing the tags. After one last check of the office, she left, heading for Botany. 

It was quiet in there.

Ali made her way to the back. David sat curled in his chair. From the ragged look on his face, someone had told him what had happened.

“I’m sorry,” she said, her voice thick. His distress was palpable. “I’m so sorry.”

“He tried,” David said, his voice breaking. “I know he tried.”

Ali’s lip wobbled. She dug her hand into her pocket. “You should have these.”

He looked up at her, his eyes falling on the silver in her hand. He stood, taking them from her. She watched him run his fingers over Evan’s name, lips moving silently. Ali held out her arms, a silent invitation, and the next thing she knew she was on the floor, David Parrish sobbing into her collar, her own tears falling softly in his hair.

She knew loss like this all too well. The memory came like a freight train. 

_She was frustrated. Math was her favorite subject, her favorite thing, something that came easy. Most of her classmates went to her for help, instead of their teacher. But for some reason she just couldn’t get this problem, couldn’t get the polynomial to factor and she threw her pen on the table in disgust. Her mom was working – something big and time consuming from the circles under her eyes – and therefore couldn’t ask for help though her mother said she was atrocious with numbers. Given it was a Saturday, Ali was at the house with nothing but her homework to keep her company._

_A break. She needed a break._

_With her cup of tea in hand (she rarely did homework without tea) she stepped into the living room and looked at John. She got her mathematical mind from him. Her mother was proud of that._

_“A little help would be nice,” she told the photo. He didn’t say a word. He never did._

_The doorbell rang as she headed back to her homework. Leaving the mug in the kitchen, she changed course for the door. A quick peek out the front window showed a dark vehicle – government plates – and she opened the door. Joe Webster, he mother’s boss, stood on the porch. He took his ever-present sunglasses off. His eyes were red._

_“Joe?” she said in a small voice. “Where’s my mom?”_

_“I’m sorry, Alison,” Joe said. “I’m so sorry for your loss.” He handed her a black thing, about the size of a wallet._

_Ali opened it to reveal her mother’s credentials. The world seemed to stop and tilt sideways as she realized what Joe was telling her. “No,” she muttered, “no.” Her breathing became sobs and her legs gave out. Joe caught her and she sobbed almost hysterically against him, Nancy’s badge holder clutched in her hand. She knew her world had shifted completely._

She was no stranger to that. But even then her world hadn’t stopped tipping.

_Ali had had a week and a half to pack up things to move with her to wherever she was going – no one had told her exactly where she was headed. The rest of the house was packed and labeled, to be put in storage, Joe told her. And then he couldn’t tell her anymore because he simply didn’t know._

_Her bags were packed, the boxes bound for storage on their way, and a county Children’s Services representative was waiting with her on the porch. Angela England had been with her since the funeral, helping her and trying to get her to talk about what had happened. Ali hadn’t spoken much to anybody since watching Nancy’s casket be lowered into the ground, clutching Joe’s hand like a lifeline. The house had been put up on the market, but no one had told Ali where she was going._

_Until then. An Air Force representative was coming to get her. Rumor was that she was going to live with her father. Wherever he was._

_An older SUV that had seen better days pulled into the driveway and Ali sat up a little straighter. The wheels were turning, figuratively. The vehicle came to a stop and both front doors opened. The driver was an older man with gray hair, the other a mid-thirties with brown hair and glasses. Both headed for the porch. Angela stood; Ali wanted to lock herself in the house._

_“Miss England?”_

_Angela held out her hand to the silver-haired man. “Nice to meet you…?”_

_“General O’Neill,” Jack said. He looked past Angela had Ali. Her facial structure must have been more from her mother, but her eyes were definitely John Sheppard’s. “That her?”_

_“That’s Alison,” Angela confirmed. “She hasn’t said much since the funeral.”_

_The brown-haired man walked back them and sat on the porch swing by Ali. She moved over for him, sliding the bags on the porch along with her. She might have been slightly overwhelmed by grief but she wasn’t rude. She was well-aware that the other man was watching them, though he was trying to not make it obvious._

_“I’m Daniel,” the man said._

_“Alison.” She looked over at him. He didn’t seem the type to be in the military. The other one, sure, but Daniel looked…different. More like he wasn’t used to..not being in the military. “You two from the Air Force?”_

_Daniel smiled a little. “Yeah.” He took a deep breath. “We’re going to take you to your dad.”_

_Which was just damned weird for her, that the guy in the photo was an actual man. And she was going to live with him. And he was an absolute stranger to her. She should have been excited that she was going to meet her father, that she was going to live with him._

_But she wasn’t._

_Because she had, in essence, traded her mother for her father. Which didn’t seem quite fair at all, even in the world view that life wasn’t fair._

_“You ready to go, kiddo?” Jack said from the steps. Angela was in the driveway, unsure whether to hover or say goodbye._

_Ali didn’t bristle because her mom had never called her ‘kiddo.’ She normally would have hated it, but it seemed right coming from him. When she really looked at his eyes, there was a sadness there, like he knew exactly what she was going through. That or he was really good at empathizing._

_“We’ll get these,” Daniel said, handing Ali her backpack. He and Jack took what other belongings she had and loaded them into the vehicle. Angela stood awkwardly to the side._

_“Bye, Alison,” Angela said, tugging Ali into a hug. The younger girl relaxed into it after a couple seconds. The CSR didn’t say anything when they parted, simply smiling encouragingly. Ali gave the woman half a wave and looked at the house again. Maybe it was better that she move out, maybe it would help the hurt. There wouldn’t be so much to trigger memories. She’d been fighting that since she’d first seen Joe on the porch._

_Still didn’t make it any easier to climb into the backseat of the SUV._

_“You all set?” Daniel asked from the front, twisting around to look at her._

_“Yeah,” she said. She looked out the side window as they backed out of the driveway._

_“I’m Jack,” the main in the driver’s seat said, glancing at his very quiet passenger in the rearview._

_“Ali,” she said, tugging her backpack closer. “So, you’re taking me to John?”_

_Jack flinched a little at the use of Colonel Sheppard’s given name from his own child; Daniel half expected it and was more prepared. Ali didn’t notice a thing, watching the rest of her old town fly by the window._

_“We’re kind of…the transit people,” Jack said. “We’re taking you to the people who are going to take you to your – to John.” Daniel’s pinch on his leg had him modifying his statement. She didn’t notice the blunder._

_“He’s not in the country?”_

_Daniel, still turned around to face her, nodded. From what the CSR had said, this was the most that Ali had spoken in days. Then again, Daniel could remember when his parents had died, how he hadn’t spoken except to know what was happening. Less confusion in an already confusing time was what he’d been after. Ali was doing the same thing. The more she knew, the more solid her world was, though it was still tipping badly at the moment. What she needed was something to hang onto. He could help with that when they got back to base._

_“He’s pretty permanent at the base he’s at, so we’re going to fly you out to him,” Jack said, hoping the illusion of overseas travel would hold until they reached Cheyenne Mountain. Then it would be a different kind of travel._

_“Okay.” Ali rubbed her eyes._

_“You can sleep if you want to,” Daniel said gently. Grief wore a person down faster and easier than anything. “It’s a bit of a ride.”_

Which, when all was said and done, was an understatement. But if it was going to help David, then she’d use every bit of knowledge she had when it came to losing someone. The first step was having someone to cling to. He had that part down. 

He hadn’t moved in a while, so Ali was thinking he was well and truly temporarily wore out from everything. She gently pried his fingers away from Evan’s dog tags, using dexterity she hadn’t used since piano to get them so they hung like a necklace again, instead of a lump of silver. Carefully, and moving slowly so as not to wake the man currently slumped against her, she draped the chain over his head and down. She wiped some more tears from her eyes, sliding the tag beneath David’s uniform top so that it settled over his heart. Right where she knew he needed it most.

* * *

Lieutenant Colonel John Sheppard may have been utter crap when it came to talking about emotions, especially with his own kid, but his instincts were usually right. Even if his parenting skills were a little rusty, they were still working. Which was why he was really glad he’d found a couch in an empty part of the city that had once used as housing. It was definitely more comfortable than the cot he’d almost broken his back on when Ali had first arrived.

Losing Evan, especially so soon after Ali had lost her mother, and nearly Stackhouse, was bound to bring up some unpleasant memories for the girl.

Needless to say he wasn’t surprised when his door chime rang late. Atlantis beat him to opening it and, confirming his instinct, there stood his daughter. Well, what of her he could see considering she was carrying her pillow and a DIY tie blanket and a…green…stuffed…thing… He let her in, and she ambled over to set her things on the bed. When the door was shut, he turned to say something and found himself with an armful of shaking teenage girl.

This was one time he hated being right.

“Easy,” he murmured, stroking her hair. It was down, for once, and still damp. “Brings up a lot, doesn’t it?”

She nodded against his chest. “I just – Can you – Can you just hold me? Please?”

John nodded, a small part of him positively gleeful that she had come to him. “Can we sit though?” Which made him really grateful he now had a couch, though it took up an absurd amount of space. 

It didn’t take long for John to situate himself and then have Ali snuggled against him, her head on his chest, the green stuffed thing named Edgar in her arms and the two of them under the DIY blanket. He was pretty sure she’d really relaxed because she’d found his heartbeat beneath her ear.

“Mom and I used to do this.”

The soft admission took John a little by surprise. “Yeah?” She was just like him in some regards, most important being if you waited long enough, he’d start talking. Ali was apparently no different. 

“Yeah.” She attempted to burrow further into him. “One of us would have a bad day, and just need to…snuggle.” Nancy had called it “reaffirming that she and what she loved was still there” and Ali had called it “plain ol’ snugglin’.”

John stroked her hair softly. “More like a bad month, right?”

She snorted. “It sucks.” She paused. “Makes me think of stuff. Mostly about mom and when she died. The aftermath.”

He didn’t want to push her but wanted her know he was more than willing to listen. “You wanna talk about it?”

Ali took a deep breath. And then another. John was starting to think she’d either gone to sleep or wasn’t going to talk to him when she finally said, “It was a Saturday.”

He didn’t need to ask what “it” was that they were talking about. Letting her go at her own pace seemed the best thing to do.

“I was doing homework in the kitchen,” she said, trying to burrow closer. John was almost worried he’d popped a rib or two out of place. “Then the doorbell rang. It was Joe, mom’s boss.” She gave a little laugh. “I didn’t want to believe him. I really didn’t. Kind of official though when they lowered her. No coming back.” She chuckled again, more humor in this one than the first. “I had a county Children’s services rep at the house with me, starting the night of the funeral and going until I went with Jack and Daniel. Those two were great.”

John’s hand stopped at the last comment. Jack and Daniel had picked her up? He thought of the last time he’d seen General O’Neill, and decided that either someone had majorly screwed up or Ali and her situation had gave them a trip down memory lane that wasn’t pleasant.

“How long were you at the Mountain?” John asked. He was in an interesting position – she was talking her way through the time when she was transitioning between one parent and another, between one life and another, and coping with death on the fly. Not only was he learning more about her, he was also helping her sort through some of the emotional things she’d been carrying with her.

“Four days, I think,” she said. “It was weird. A little claustrophobic being underground, but the biggest thing was when Jack and Daniel sat down with me and basically explained everything they could about the Stargate and what they did. But I never saw the thing. I met Teal’c, and he was really cool, except that every time he saw me he called me ‘AlisonSheppard’ and wouldn’t even try Ali.” She said the last part with a chuckle. “I spent a lot of time with Daniel.” She hunched her shoulders a little; John went back to stroking her hair. “I was really quiet after mom died, and I didn’t want to talk about it. So Daniel did most of the talking. Talked about Atlantis, about you, and about loss. He talked about when he lost his parents and how the most frustrating thing was not knowing what was going to happen next. I mean, you were already off-balance enough because you lost a loved-one, and to have your future, even if it was just the next day, up in the air…It’s completely crazy.” She shivered; John pus his arm around her and took her hand when she reluctantly released Edgar. He figured she thought he was a better thing to hold onto in the end. “Then he told me he went through kind of the same thing when he lost his wife.” 

John prayed Daniel hadn’t told her _how_ he’d lost his wife.

“I asked him how he got through it,” she continued softly. “And he smiles and pulls out this old book and I’m thinking, great, he read this book and was comforted and I’m thinking it’s some off-world Bible or something, and he opens it and it’s a photo album. He says, ‘My family helped me,’ and there’s a picture of his team. And he says, ‘My family always helps me.’” Ali sniffled. “I didn’t think I had family anymore. Then I cam here. It’s not what I expected. You’re not what I expected. But we’re working on it.”

He swallowed the lump in his throat. “Yeah. Yeah, we are.”

She snuggled closer still and John thought his ribs were going to have to start moving to accommodate her. Not that he minded. He was enjoying the closeness.

“Ali?”

“Yeah?”

“Not that I’m complaining, but why do you have my last name?”

She turned enough so that she was looking up at him, even if it he looked upside down and she had a better view of the inside of his nose. “I asked mom the same thing when I got old enough to realize that my last name and hers weren’t the same.” She smiled a little. “She wanted to give me something of you, to tie you to me. So that’s why I’m a Sheppard.” Her smile widened. “My full name is Alison Marie Holden Sheppard. She tied me to both of you.”

John thought he’d stopped breathing for a moment. “You know that Marie – ”

“Is your mother’s name?” Ali finished for him.

It had seemed that Nancy had tied their daughter to both sides of her family. All without John ever knowing it.

The silence, comfortable instead of awkward, grew between them. He should have known it was a prelude to her dropping an emotional bomb.

“Do you miss her?”

John tweaked her nose, prompting a grin, and thought carefully about what he was going to say. He then wondered if their relationship could stand this conversation. Either way, she deserved his honesty. Which meant he needed to think about this.

He’d loved Nancy, he really had. They’d talked about children, about long-term goals and aspirations. But John had loved his job, first and foremost, and loved flying. If he’d known he’d had a child, would he have given it up completely for a family? The answer: He wouldn’t have given it up completely, but he would have made damn sure he was closer to home and definitely around more. He’d missed a lot, missing out on watching Ali grow up, and though it was a cruel twist of fate that had dropped her to him, he was glad to have her in his life.

“I do miss her,” he said. “And I loved her. I loved your mother, Alison, I loved her enough to honestly let her go because she was too good to be second best to anything, especially the Air Force. I love flying, it was what I’ve always wanted to do since I was little. I couldn’t be the man she deserved. But yes, I miss her.”

Ali could barely see his eyes from her position, but knowing John and how he was at expressing emotions, coupled with the sincerity he was speaking with, she knew he wasn’t bullshitting her. Which made her tear up. And so was John.

“You look like her,” he said. “You have my eyes, my smirk, and God knows you have my stubbornness, but you look like your mother.”

And that meant a lot coming from him. She couldn’t help it; she let a few tears escape. He wiped them gently away with his thumb. 

She held the moment for a few more seconds and then sat up, a watery smile in place and sat cross-legged on the couch, facing her father. John moved his ribs back into their natural position and copied her pose. It was a good thing he was skinny otherwise he would have had issues with keeping his ass on the cushion. She moved Edgar into her lap. He pointed the green…thing.

“What exactly is that thing and where did you get it?” he asked, genuinely curious.

“Not really sure what he is,” she said with a shrug. “But he was a birthday present-slash-hospital gift when I had my tonsils out. From Gramma Holden.”

“Your mom’s mom?”

Ali nodded. John briefly remembered meeting Nancy’s mother and walking away with the “there but for the grace of God” feeling. The woman had been a force of nature. She and Rodney would have gotten along wonderfully.

“I don’t have my tonsils either,” he said with a shrug. “Don’t have my appendix, either.”

“Ooh,” she said, smiling. “I broke my ankle. Spent three weeks in a cast.”

John arched only one eyebrow. Did she really want to play this game? Did she not realize what he did for a living? Still, this would be fun and interesting, not to mention chase away some of the gloom from the day. Carson had started his autopsy but hadn’t found anything unusual so far, so John had gone to decompress.

So far it was working.

Then she leveled his own “bring it on” look back at him. Another reminded that she was indeed his daughter.

“Broken collarbone.” He leaned forward. “Running track.”

“That’s got a good story behind it,” she grinned. “Dislocated pinky. Eighth grade. Dodgeball.”

“What the hell were you usin’ for balls?” John asked her, his face absolutely priceless.

She held up her pinky – it pointed in a decidedly 45 degree angle away from the rest of her hand.

Again, his “holy shit” expression was priceless. She grinned broadly and let him inspect her pinky. “You still have the X-Rays for this thing?”

Ali laughed. “In storage in Colorado.”

“Jack needs to ship some boxes,” John said, settling back. Ali’s chuckle died slowly. “What?”

“Can he?”

“Can he what?” He was mildly confused.

Ali turned shy, rubbing the edge of Edgar’s ear. “Can Jack ship some boxes out?”

He wasn’t sure what had made it possible to have Ali and General O’Neill on a first-name basis, but if that was the case then John was willing to be good money that Jack would make almost anything happen to make Ali smile. Especially if she’d had a rough time at the Mountain.

“Yeah,” he said. “Jack can send some boxes.” _He’d better be able to._ “Did you have anything specific in mind?”

She bit her lip, blushing. “The ones with photos.”

His mouth formed an ‘O’ of understanding. Then he brightened. “I wanna show you something.” He got up, heading to the closet. When he came back with a shoebox, Ali had an inkling of what he was going to show her. Still, she let him run the show. He got back on the couch and sat cross-legged again. He opened the box. Handed her the first picture.

It was of John, dressed in his field gear, and sitting on the steps of the Gateroom. Well, he wasn’t sitting so much as lounging, sunglasses on and, for all intents and appearances, looked so boneless that he was probably asleep.

“Sleepin’ on the job?” she asked.

“I was tired,” he defended, pleased once more to see her smile. The next photo he held up got an “aaww” – it was John and Rodney in the back of a puddlejumper, shoulder to shoulder, Rodney’s left arm in a sling and John’s right leg splinted and on the bench, opposite of Rodney. They were giving the camera a “what the hell” look.

John sucked in a breath at the next one. It was him and Lorne, back to back and grinning. It had obviously been posed, but the smiles, even John’s, looked natural. And Lorne looked so young. Ali bit her lip, taking the photo.

“Can’t believe he’s gone,” she said softly.

“Yeah,” John said in agreement, shuffling through the shoebox. The pictures had been Kate Heightmeyer’s idea, a way to make Atlantis seem less like an abandoned city and more like home. Real people, real memories. If John looked at the bottom of the pile, he’d find some of Aiden. Maybe one day he’d be able to get them out and not feel so much guilt and pain. Maybe then he could remember and honor Aiden better by telling Ali. Maybe one day. “Is Parrish okay?”

Ali froze. What, exactly, did he mean by that? Did he know? She looked at him oddly.

“Just meant that he and David are pretty close.” John winced. “Were pretty close,” he amended softly. He gave Ali another photo. 

It almost broke her already bleeding heart.

It was in the same vein as John and Rodney’s, only there were no apparent injuries. Both men were shoulder to shoulder, dressed in field gear and streaked with mud. David’s head was on Evan’s shoulder, Evan’s cheek in David’s hair, both fast asleep. The back of the photo had neat handwriting that said, _David & Evan 4 days on MX4-839 diggin ditches_

Ali wiped under her eyes. “He’s doing okay. But it’s hard. They were really close.” It was an understatement as she remembered what she’d gone through when she’d lost her mother. It seemed so fresh, more poignant recently than when it had happened. It had felt surreal then, like it wasn’t happening to her, like it was somebody else’s tragedy and she was an outsider, an observer. Sometimes it had gotten difficult to breathe, the pain was so intense. “It’s so hard.”

They lapsed into silence again, broken when Ali yawned.

“Been a long day, kiddo,” John said, allowing the words to roll off his tongue. Them dang parenting instincts were kicking in again.

She held Edgar to her chest and picked at the blanket. “I don’t want to be alone.” Which was why she’d come in the first place.

From John’s point of view, she looked small and vulnerable. He gently took her blanket and Edgar, swapped his pillow out for hers, and folded down the covers. 

“John, I don’t - ” she stammered and then moved when he raised his eyebrows at her. He dug out another blanket for him and flopped his pillow on the couch.

“John?”

There was vulnerability in her that he hadn’t seen before and wasn’t sure what to make of it. 

“Will you sit with me? Until I fall asleep?”

He didn’t hesitate in moving toward the bed; she moved over enough so he could sit down. She curled on her side, Edgar tucked under her chin. She relaxed further when he started rubbing her back. He was prepared to sit there as long as necessary, all night, even. He thought she was asleep when she murmured, “I needed this.”

“Yeah,” he agreed. He had needed it too, though he wasn’t entirely sure that was all she was talking about.

“I needed this that first night,” she said. “I needed you.”

John swallowed through a dry throat, his hand never stopping on her back. 

“I wish you’d been there,” she mumbled before dropping off.

_Yeah,_ he thought, _I wish I’d been there, too._

* * *

John had never felt relief so deep before. This permeated his bones.

It wasn’t Lorne’s team. It _wasn’t_ Lorne’s team. 

After putting his head down on his desk and giving in to the intense sense of “Thank You Somebody!!” he sat up and looked at the bottom drawer. The drawer that held the dog tags of the team he and the rest of Atlantis had thought they’d lost. He opened the drawer, carefully taking out the tangled pile that was SG-2. Yet, last time he’d looked at the personnel roster, there were four people on the team. 

Evan’s tags were missing. 

John chewed his bottom lip, filing the information away to the back of his mind because what he really needed to focus on now that he wasn’t going to have to plan a funeral service, was devising a rescue mission, once he found out where they actually were. He stood to leave, wondering where exactly those dog tags had wandered off to.

* * *

Ali, having been in the right place at the right time, had been positively floored when she’d heard that the scorched bodies in the infirmary weren’t Evan and his team. She covered her face with her hands, intensely relieved, wanting to cry because it felt so good. A part of her was selfishly glad she wouldn’t have to learn once again, to say goodbye to another person that had become family, that she didn’t have to lose someone else. Once that had been done (and a few tears leaked out) her emotional state swung inexplicably toward David, who was most likely holed up in his lab as a coping mechanism, immersed in the Earth plants as a comfort. Considering he wouldn’t emerge for a long, long time unless someone made him (Ali routinely did – she made him come out, semi-socialize, and eat) she headed back the way she’d come and started, somewhat conspicuously for the Botany department at nothing less than a sprint.

She careened around the corners of Atlantis, slapped a palm over the door mechanism, and only slowed down when she was among the rows of plants. She calmed her breathing instinctively and made her way toward the back. No surprise, David was sitting in his chair in a patch of sunlight, looking at the plants he loved. 

“David.” 

He jumped, turning bright eyes toward her. He’d been crying recently. As someone who’d recently had a loved one die, she could completely empathize. She ignored the small part of her that was jealous that David got to have Evan back, when she couldn’t have her mother again, that Nancy had been taken from her with no chance of return. 

_You’ve got John now,_ the voice in her head that sometimes made her want to scream, rationalized. _You got one parent for the other. Not fair, but it’s what you’ve got._

“Carson finished his autopsy,” she said, keeping her voice steady. 

There was a spark of hope in David’s eyes. It was weak, but it was still there, and Ali latched onto it. 

“It’s not them,” she said softly. She smiled, blinking back wetness. “It’s not Evan.”

David’s eyes turned hard for a moment, as though scrutinizing what she was telling him and trying to find the lie within it, searching for the fluff she was feeding it. She could tell the moment he realized it was the truth. It was almost comical in a way, a twenty-something, almost thirty, probably, man launching himself at a sixteen-year-old girl and latching onto her like everything was once again tumbling to the ground. And Ali, knowing what it was like to be broken, wrapped her arms around him as best she could and resigned herself to having stiff muscles from so much time on the floor. Out of the whole thing, what made her smile was the chain she could feel through his shirt and hers against her collarbone. Evan’s dog tags. 

That and the knowledge the man would be coming to claim them.

* * *

“I think I need a break,” Ali said, sinking into the chair in front of John’s desk like it was her job. She rubbed her eyes. What she really needed, and she knew she’d thought this more than once, was a longer break between crisis. But that never seemed to happen, really. Her mother dying had rolled into moving to the Pegasus Galaxy to live with a father she’d never met before, that had compounded into John attempting to morph into a bug (or something, she really wasn’t quite sure) which had been followed shortly by her first trip off-world that was also coupled with a Wraith encounter, which was had rolled into the silent treatment from her to John in which John had lost focus on a mission and fallen down a hill, which, not even a week later, had been eclipsed by her seeing people before they were going to die, Stackhouse _dying_ at one point, only to be brought back by Carson and his defibrillator with the aid of her panic-induced CPR, and everything rounded off by Evan Lorne and his team being burned to death, but really, the Genii were simply planning a coup and wanted some help. _That,_ according to John’s ramblings, was more of a headache than it was really worth, but it kept Elizabeth happy, and it fostered good diplomatic relations, so he had no choice but to go with it.

All of that considered, Ali was feeling a little battered. John, while probably sporting a headache, was used to the constant ebb and flow that was day-to-day Atlantis, and it was considered a good day if the city wasn’t sinking and nobody was attacking. Ali needed a little more calmness in her life. Just a little.

_And I used to wish for excitement,_ she thought ironically. _Then I moved here._

John looked up from the report he was reading and contemplated the girl in front of him. His daughter. Some days, that still blew his mind. But he could see what she was hinting at. Ali looked worn around the edges, like she needed some quiet time. Something peaceful. 

The folder to his left caught his attention. It was in his “upcoming” pile. McKay and Griffin heading to the mainland and back. Short, sweet, simple, and the Athosians had this…calmness…about them that, if Ali had enough time to meditate, would probably do wonders for her. Not that she couldn’t meditate with Teyla on Atlantis, but it did good ever now and then to get out of the house, so to speak. 

_Out of the house and away from the parents,_ he thought with a smile. “Ali, how about a trip to the mainland?”

She tilted her head at him. “With you?” She hadn’t had another flying lesson after the one he’d given her when she’d first arrived. 

“Not quite,” he said. “And not a flying lesson, either.” He enjoyed sharing something that was fundamentally a part of him with her, and would make a note to schedule it sometime soon. “McKay and Griffin are heading out to check something. You could ride along, if it’s alright with McKay.” Which, if Ali used her hazel eyes to her best advantage, would get Rodney to cave on almost anything, was most certainly going to happen. 

“Sweet,” she said. She was already planning on how to convince Rodney to maybe teach her some practical uses of physics, maybe more on how to wire a jumper. Some of the systems couldn’t be that difficult to transfer to Atlantis – it was a little cold in her room. And, well, why ask someone to do it for her when she could ask someone to teach her?

* * *

Rodney realized that Ali was indeed John Sheppard’s daughter because the look she gave him was purely her father’s crafting. And John had tried to use it before, usually on alien diplomats, with varying degrees of success. There was no fighting Ali’s. And he knew Griffin wouldn’t mind the extra company since he had yet to actually meet Ali. She was still a conundrum to certain people. When new Marines arrived, they assimilated quickly, mixing in with the old and standing out until they’d circulated enough to be well-known. Ali, on the other hand, was a little more selective, even if by accident, and the only real public “view” people got of her was in the cafeteria or when she was wandering the halls of Atlantis looking for something to do. Most of the botanists knew her, simply because she spent quite a bit of time with David Parrish.

The ride going out was fine – Ali slept for most of it, part of it being it was the first real downtime she’d had in a few days, especially after the latest escapade with Stackhouse. After landing the jumper and walking to the settlement, she was in for a bit of surprise.

The Athosians weren’t quite what Ali was expecting. She’d been thinking that they were all more or less like Teyla – calm, collected, very meditative, and all together relaxed. She definitely hadn’t been expecting to be surrounded by a dozen or so children of various ages and looked at with such intensity. 

It was Halling who rescued her from the rush; the children happily followed in Griffin’s (their pilot for the day) wake and Ali figured that before he really knew what was happening, he was being roped into playing some sort of game with them. From the happy shrieks and mad scrambling, it was something akin to tag.

“Wow,” Ali said, tucking a piece of her hang behind her ear. “They’ve got some serious energy.”

“They’re making up for the time when they were cooped up in the halls of Atlantis,” Halling said. “I am Halling, leader of the Athosians while Teyla is in Atlantis.”

“Alison Sheppard,” Ali said, sticking out her hand.

Halling looked at her oddly. “Has Teyla taught you the traditional welcome of our people?”

She shook her head. She froze slightly when Halling stepped a little into her personal space and gently touched his forehead to hers. It was a short contact, but Ali shivered. It was very personal. 

“Sheppard, did you say?”

She tugged the cuffs of her long-sleeved shirt over her knuckles, a fidget. “Yup.”

“You’re the Colonel’s daughter?”

Something unknown curled in her belly at his wording. The Colonel’s Daughter. It sounded like it should be capitalized. Did it really matter who her father was? 

“He’s a good man.” Halling waited until she was looking at him before continuing. “He was the one who rescued us from the Wraith, gave us safety within Atlantis.”

Ali had heard bits and pieces of that story, but never the entire thing. Then again, most of John’s life in the city went like that; pieces, but never the whole. And always from another source. 

_Not like you’ve been exactly open with your own life,_ the voice in the back of her head whispered nastily. _Think about it. You want him to open up, but you’ll probably never do the same. Because you don’t want to get hurt again. You don’t want him to leave again._ Which, technically wasn’t true, because John had never been around to leave. He’d always been missing.

“He is a good guy,” she said softly. “But I don’t really know him.” She looked at Halling’s soft brown eyes. “My mother didn’t tell him that she was pregnant with me. He only found out a little while ago that he had a daughter. Only because my mother died.” There was still a sting to her words, but not so much the deep ache that had previously been there. If she were honest with herself, it was probably because she was more used to John, more used to the fact that her _father_ was there and was really the only blood family that she had left. 

Truthfully, it was getting more and more difficult to keep thinking of him as ‘John.’ 

“I think you need him as much as he’s needed you,” Halling said, laying a hand on her shoulder. “And I think your mother would understand.” He gave her shoulder a squeeze, pointedly ignoring the blank shock on her face. “Good to meet you, Alison Sheppard.”

The shouts of the children (and Griffin) returning were getting louder as Halling turned to go. Ali took a moment for herself to simply breathe and regain some semblance of composure before turning around and, like déjà vu from when she’d arrived, was nearly mauled by a group of happy children. 

“Griff says you’re John’s girl!” one of the small boys to her left said excitedly. “Does this mean that you like the same things he does?”

“Football? Do you like football?”

“Catch?”

“Do you like flying?”

The questions came from every angle, stunning her momentarily. She looked over their heads at Griffin, who had the decency to be rubbing the back of his neck, a red hue tinting his cheeks. It was one thing for her to talk about the fact that she was John Sheppard’s daughter with Halling, but quite another to be speaking with the gossip wagon that was small children. And they were all so perky. No wonder Rodney had issues with them.

“Yes, John’s my dad,” she said, stumbling over the word and hoping none of them noticed. A few of the older children gave her an odd look but she plowed on. “No, I don’t really like football, I used to play softball so I do like to play catch, we both like to run, and he did teach me to fly.” From the excited looks and awed expressions, John was very well-liked and she’d said exactly the right things. 

Griff tapped his earpiece and motioned to her that they had to leave. Ali told the children she’d be back when she could (“Yes, maybe with John”) and found it a little difficult to walk away from the free-ness that was young children. 

What was a little more difficult to walk away from was the warm feeling in her chest at the phrase, “Yeah, John’s my dad.”

“I’m sorry,” Griffin said, as they were walking to where he’d parked the puddlejumper. 

“Don’t worry about it,” Ali said, meaning every word.

* * *

The ride coming back was a different story than the one going out.

Ali had a white-knuckled grip on the sides of her seat, staring through the front of the jumper at the expanse of blue ocean that, with every bump of turbulence, seemed to get a little closer than when they’d started the trip. 

“You might wanna put a seatbelt on, Ali,” Rodney said, his own face as pale as hers. He was a little more composed; she was freaking out royally on the inside. 

The jumper bumped and rocked. It was more turbulence than Ali had ever experienced, even when she’d flown from one side of the country to the other during a vacation with her mother once. Which, in her opinion, had been an absolute disaster.

She bit her tongue as the jumper nosedived, heading straight for the wall of blue. Fumbling hands tried to cinch an already tight seatbelt a little closer, pressing on her midsection. Not that it mattered much anyway. The puddlejumper plowed into the ocean with the grace of a cannonball and she jerked forward, biting her lip bloody so as not to scream. She ended up with a case of whiplash anyway, smacking the back of her head off the seat and feeling decidedly hazy, fighting double vision and blackness. Her stomach hurt where the seatbelt had dug in on impact. Well, it hurt anyway with nervousness and anxiety, but that didn’t really count at the moment. 

_Least I’m not on the floor,_ she thought giddily. It was a safe bet to say she wasn’t really all that with it at that point.

Rodney touched his forehead gingerly. Slight double-vision revealed blood on his fingertips and, after making sure Griffin was okay, turned in his seat to look at Ali. She was massaging the back of her head, but looked alright, otherwise. Pulling himself together, he contacted Atlantis. Ali was a little focused on other things to hear much of the conversation. Focus being the key word.

_Am I concussed?_ She grinned. _Cool…_ Which most certainly did confirm that she was probably _not_ okay.

_”Is everyone alright?”_ Zelenka asked, once Rodney had given him the basics of the situation. Already 1200 feet deep and sinking at 20 feet per minute were not happy numbers to be working with. Colonel Sheppard was not going to be a happy camper, either. 

“We’re fine,” Rodney said, looking once more over his shoulder at Ali. She pulled it together enough to give him a thumbs up. He looked back, paling as the viewscreen in front of him began to crack. The systems on the panel flickered, the screen splintering ominously. The open connection with Atlantis died with the puddlejumper systems but Rodney was already moving, out of his seat and herding a confused and stumbling Sheppard toward the back of the puddlejumper. 

“Griff!” Ali stood by the rear door of the puddlejumper, arms wrapped around her middle and simply watched in a disconnected stupor as Rodney and Griffin tried to convince the door separating the front portion of the jumper with the back to close. The front port didn’t look so much like a window, but more like an intricate spider’s web, wispy thin cracks appearing everywhere. If it hadn’t been so deadly, it might have been beautiful. 

“Griffin,” Ali murmured, shaking as water leaked through the front viewscreen. Griffin gave Rodney a shove backward and the door slammed shut. There was a thud, presumably as the viewscreen broke and Ali felt tears prick her eyes. Griffin was gone. She shivered, the temperature in the lifeless puddlejumper beginning to drop, struggling to comprehend the fact that Griffin was undeniably gone.

“You okay?” Rodney asked, breaking the silence.

“I’m fine,” she said automatically though she was feeling anything but. She looked at him, noticing the blood on the side of his head. “What about you?” She touched her own forehead as an example. 

He reached up and gently touched the lump, his fingers coming away red. “It’s fine.”

Lies. And they both knew it.

Ali sat, hunkered on a bench and shivering, arms wrapped around her unsettled middle trying to both keep warm and give herself some comfort. She alternated between watching the floor and watching Rodney mumble his way through attempts to send a distress signal and put some life back in the dead puddlejumper. Maybe get them some heat. All while through a concussion. She had her own headache, as well. The cold was helping nothing.

She pulled her legs up, curling into a ball as much as possible. She looked up and froze, the breath catching in her lungs. On the other side of the jumper, on the other bench across from her, was her mother.

Nancy smiled at her daughter.

“Mom,” she murmured, glancing at Rodney, who was staring at the center of the floor like it was the most fascinating thing he’d ever seen in his life. When she looked over again, Nancy was gone. Ali took that as confirmation that she was either indeed concussed or going insane. Neither was comforting.

“You’re not crazy, baby.”

Ali thought her heart was going to stop. Nancy was sitting on her left as though it were an every day occurrence, like they were back in Colorado and sitting in their living room watching a movie. Like there was nothing wrong and Nancy wasn’t dead. She could practically see the fireplace across the puddlejumper, across the room. It produced a pang of homesickness so bad that her eyes teared.

“Mom?” she murmured again. Then she glanced at Rodney. She really didn’t need an audience for this.

“Don’t worry about him,” Nancy smiled. “He’s got his own hallucination to deal with.”

_I’m hallucinating?_ she thought. _Sounds better than going crazy._ “You’re a hallucination?” Even as she said it, she felt her stomach turn heavy. She’d been wishing for a miracle, honestly, something more definitive. Maybe a ghost. But along with the realization that she was hallucinating, the fact that Nancy was still gone remained.

“Yes, baby,” Nancy said. “I’m here to help.”

How, exactly, was a hallucination of her dead mother going to help the situation?

“Alison?”

Ali looked over at Rodney. He didn’t look good. His eyes were slightly glazed, wide and wild. He was concussed. And hallucinating, according to her mother.

“Are you okay?” He kept glancing to his right.

“Yeah,” she said, shivering.

“I’m hallucinating,” he blurted.

“Makes two of us,” she muttered. 

Rodney moved to sit beside her, on the side that Nancy wasn’t occupying. He moved his arm, slowly at first, as though he wasn’t sure what he was doing or how she was going to react, and finally put it almost hesitantly around her shoulders. She leaned against his side. Rodney was John’s best friend. Not quite her father, but a member of his Atlantis family, so a member of hers.

“I’m going to get you out of here,” he said softly. She could hear the promise in his voice. 

Ali looked over at her mother. “I know.” And she did. Rodney would do his absolute damndest to get them both out. She just hoped it would be enough.

* * *

They were doing relatively well until the water started leaking in the temperature plummeted.

Ali stood on the bench, watching the water level rise, slow but steady.

“Ali.”

She whipped her head around, looking her mother almost in the eye. They were blue eyes, like Rodney’s, instead of hazel, like her and John’s. 

“John’s coming for you.” 

She knew that. Really, she did. Rodney had made contact (sort of) with Atlantis. John and Radek were on their way down. She and Rodney just had to hold on that long. And it was getting harder and harder to stamp down on the panic and hopelessness. Rodney’s random outbursts to “Sam” weren’t helping her nerves.

“I miss you,” Ali blurted, shivering and tearing up. “Why did you leave me?”

“Oh, baby,” Nancy said, reaching for Ali’s hand. If she concentrated on it, she could have swore she felt it, even though it wasn’t real. “I didn’t want to leave you, but I didn’t have a choice. Sometimes things happen, and then all you can do is do the best you can with the consequences.”

“You left me.” Ali’s breathing hitched. “You left me by myself.”

Nancy’s blue eyes softened. “I didn’t leave you by yourself. You know how I used to say one door shut and then another would open?”

“And if one didn’t open, just bust a window and go in that way?” Ali finished her mother’s near-favorite quote with a slightly hysterical chuckle, the first of the tears tracking their way down her cheeks. 

“Exactly.” She brought her hands up to frame her daughter’s face. Ali wanted so much for those hands to be real and tangible, to hold her once more in warmth and comfort. To talk about John over dinner near Father’s day, and her birthday, and the other calendar holidays. She wanted all of that back, even if it was just for a moment. “Listen to me, Alison Marie.” Alison Marie. A Holden and a Sheppard. Two parts of the whole that she was. “Listen to me. I know it’s not fair, what happened, and, let me tell you, getting shot hurts like hell, but it hurt me too to know that I was leaving you, my baby girl, alone for the moment. Without her mother. A girl should always have her mother. And I know it’s not fair, but you’ve got something more precious than just empty space and an empty home.” She smiled. “You have your father. I know it seems a poor trade, the loss of your mother for the acquisition of your father, but John needs you just as much as you need him. He loves you, Alison Marie, even though he’s a little slow on the uptake some days,” – that got a chuckle from Ali – “but he means well. Because he loves you. You’re his daughter. And you’re a beautiful, smart, funny, and courageously strong young woman to face all that you have and come away for the better. You’re in his life, Ali, whether either of you were expecting it, and he’s let you in. Deep down, I know you want to do the same.” There were tears in the blue eyes as well. “It’s a hard road, the one you’ve been placed on, but if anyone can come through it and grow, it’s you. Alison Marie Sheppard. John’s daughter.” 

Ali’s shoulders shook with the effort of keeping her sobs quiet. She closed her eyes to concentrate on the feeling, the memory, of her mother kissing her on the forehead. 

“Every little girl needs her dad,” Nancy whispered. 

Ali opened her eyes and her mother was gone. “Mom?” She wrapped her arms around her middle and slide against the wall so that she was sitting on the bench, legs in the icy water. She didn’t care that her pants were getting soaked, that she was getting colder. What made her shake and sob was that her mother was right. Deep inside she did love John, loved him as only a daughter could love her father. And since Nancy had only been a hallucination, it was her semi-concussed mind’s way of ordering her to stop lying to herself. 

“Ali?”

She looked up at Rodney, a tear-stained shaking, absolutely miserable wreck of a girl. “I want to go home.” Her voice cracked.

Rodney didn’t have a clue what to do or say to attempt to comfort her. He didn’t know what was wrong.

Before she really knew what was happening, they were literally swimming. She was treading water, watching the ceiling get closer and closer. She watched, detached, as he argued with himself – with Sam – about whether or not to dive for the secondary release. He kept looking at her, motioning as best he could in the water at her, and the only thing that kept her floating, kept her head literally above water, was that she wanted to see John. She wanted to have more time with her father, to really cement the fact that yes, her life had changed, yes she’d lost someone, but she’d gained so much more. She wanted a second chance with the father she’d always wanted, never had, and was now gifted with.

Rodney dove under the water as her hair brushed the ceiling. The next she knew the water was rapidly leaving, taking her with it, until something latched onto her ankle, holding her against the rush. She coughed, shivering on the floor of the jumper and only belatedly realizing that she wasn’t drowning. She opened her eyes, lifting her chest and shoving hanks of wet hair out of her face to see out the open hatch of the puddlejumper. John was moving toward her, somehow walking on the floor of the ocean and miraculously not drowning.

She scrambled to her feet and ran toward him. It made her head pound, and her vision blurry (that was tears this time) and she launched herself at him, wrapping her arms around his neck as tightly as she could, her entire body heaving with the force of her sobs.

“What?” John murmured, holding her up. “I can’t understand you, kiddo, you gotta slow down.”

“Home,” she barked. “I wanna go home!” She clung tighter to him. “Please take me home.”

John was confused and it must have shown in his pause. 

“Atlantis,” she croaked, her voice cracking. “Take me home.”


End file.
